Starting phenix.real_space_refine on Wed Jul 1 23:22:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbv_34644/07_2026/8hbv_34644.cif" } resolution = 2.51 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= 0.005 sd= 0.118 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 4 5.49 5 S 18 5.16 5 C 2100 2.51 5 N 543 2.21 5 O 614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3279 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 0.68, per 1000 atoms: 0.21 Number of scatterers: 3279 At special positions: 0 Unit cell: (69.222, 68.388, 110.922, 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 18 16.00 P 4 15.00 O 614 8.00 N 543 7.00 C 2100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 76.4 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 3 sheets defined 60.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 11 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 76 through 105 removed outlier: 4.567A pdb=" N ASP A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 143 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.659A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 Processing helix chain 'A' and resid 210 through 242 removed outlier: 3.563A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 269 through 297 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 639 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: 0.33 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 743 1.33 - 1.45: 730 1.45 - 1.57: 1842 1.57 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3350 Sorted by residual: bond pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.443 -0.109 1.10e-02 8.26e+03 9.87e+01 bond pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.453 -0.111 1.50e-02 4.44e+03 5.50e+01 bond pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.446 -0.104 1.50e-02 4.44e+03 4.82e+01 bond pdb=" C21 PC1 A 402 " pdb=" O21 PC1 A 402 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 3345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 4374 2.16 - 4.33: 113 4.33 - 6.49: 44 6.49 - 8.66: 5 8.66 - 10.82: 5 Bond angle restraints: 4541 Sorted by residual: angle pdb=" C51 CDL A 401 " pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.60e+01 angle pdb=" C11 CDL A 401 " pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.54e+01 angle pdb=" C71 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 111.64 122.46 -10.82 1.65e+00 3.69e-01 4.32e+01 angle pdb=" C31 CDL A 401 " pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 111.64 121.14 -9.50 1.65e+00 3.69e-01 3.33e+01 angle pdb=" OB8 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB9 CDL A 401 " ideal model delta sigma weight residual 123.94 117.51 6.43 1.21e+00 6.80e-01 2.81e+01 ... (remaining 4536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1771 17.43 - 34.86: 149 34.86 - 52.29: 28 52.29 - 69.72: 10 69.72 - 87.15: 3 Dihedral angle restraints: 1961 sinusoidal: 778 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG A 39 " pdb=" CD ARG A 39 " pdb=" NE ARG A 39 " pdb=" CZ ARG A 39 " ideal model delta sinusoidal sigma weight residual 180.00 135.59 44.41 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 1958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 237 0.030 - 0.059: 166 0.059 - 0.089: 64 0.089 - 0.118: 30 0.118 - 0.148: 9 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA THR A 177 " pdb=" N THR A 177 " pdb=" C THR A 177 " pdb=" CB THR A 177 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA GLU A 167 " pdb=" N GLU A 167 " pdb=" C GLU A 167 " pdb=" CB GLU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ARG A 276 " pdb=" N ARG A 276 " pdb=" C ARG A 276 " pdb=" CB ARG A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 503 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.022 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE B 101 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 212 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 10 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.020 5.00e-02 4.00e+02 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 451 2.75 - 3.29: 3118 3.29 - 3.82: 5823 3.82 - 4.36: 6936 4.36 - 4.90: 11855 Nonbonded interactions: 28183 Sorted by model distance: nonbonded pdb=" OE2 GLU A 68 " pdb=" OG SER A 144 " model vdw 2.209 3.040 nonbonded pdb=" O VAL A 14 " pdb=" OG SER A 18 " model vdw 2.272 3.040 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.283 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OE2 GLU A 261 " model vdw 2.290 3.120 nonbonded pdb=" OD2 ASP B 100 " pdb=" NH1 ARG B 104 " model vdw 2.308 3.120 ... (remaining 28178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.850 Find NCS groups from input model: 0.010 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 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 : 0.009 0.124 3351 Z= 0.506 Angle : 0.964 10.821 4543 Z= 0.501 Chirality : 0.048 0.148 506 Planarity : 0.005 0.052 566 Dihedral : 14.342 87.145 1204 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.54 (0.38), residues: 410 helix: 1.88 (0.31), residues: 219 sheet: -0.75 (0.62), residues: 52 loop : 0.50 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 293 TYR 0.016 0.002 TYR A 157 PHE 0.069 0.004 PHE B 101 TRP 0.007 0.002 TRP A 173 HIS 0.002 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.51 ( 3350) covalent geometry : angle 0.96139 / 0.50 ( 4541) SS BOND : bond 0.00613 / 0.32 ( 1) SS BOND : angle 3.42459 / 2.01 ( 2) hydrogen bonds : bond 0.09123 / 5.72 ( 226) hydrogen bonds : angle 7.27625 / 5.18 ( 639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.137 Fit side-chains REVERT: A 70 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6688 (ptt90) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.6902 time to fit residues: 47.1317 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113193 restraints weight = 3997.570| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.28 r_work: 0.3265 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3351 Z= 0.143 Angle : 0.524 5.450 4543 Z= 0.272 Chirality : 0.040 0.146 506 Planarity : 0.006 0.056 566 Dihedral : 9.865 57.195 497 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 9.47 % Favored : 88.46 % 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: 2.25 (0.39), residues: 410 helix: 2.57 (0.31), residues: 220 sheet: -0.41 (0.65), residues: 52 loop : 0.59 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.011 0.001 TYR A 157 PHE 0.023 0.002 PHE A 17 TRP 0.007 0.001 TRP B 57 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3350) covalent geometry : angle 0.52230 / 0.27 ( 4541) SS BOND : bond 0.00340 / 0.18 ( 1) SS BOND : angle 1.82609 / 1.07 ( 2) hydrogen bonds : bond 0.03711 / 2.63 ( 226) hydrogen bonds : angle 5.67047 / 4.07 ( 639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.124 Fit side-chains REVERT: A 70 ARG cc_start: 0.7949 (mtt180) cc_final: 0.6788 (ptt90) REVERT: A 91 ARG cc_start: 0.6931 (tmm-80) cc_final: 0.6647 (ptp-170) REVERT: A 117 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6798 (mm) REVERT: A 228 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8838 (mtp) REVERT: A 276 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8116 (tmt-80) REVERT: B 106 GLU cc_start: 0.8012 (mp0) cc_final: 0.7802 (pm20) outliers start: 7 outliers final: 2 residues processed: 75 average time/residue: 0.6805 time to fit residues: 52.1195 Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113888 restraints weight = 4006.104| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.28 r_work: 0.3269 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3351 Z= 0.130 Angle : 0.493 5.405 4543 Z= 0.256 Chirality : 0.040 0.141 506 Planarity : 0.005 0.050 566 Dihedral : 9.389 57.155 497 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.55 % Allowed : 13.91 % Favored : 82.54 % 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: 2.54 (0.40), residues: 410 helix: 2.86 (0.31), residues: 221 sheet: -0.43 (0.66), residues: 54 loop : 0.70 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.013 0.001 TYR A 157 PHE 0.013 0.001 PHE B 101 TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3350) covalent geometry : angle 0.49251 / 0.26 ( 4541) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 1.36569 / 0.80 ( 2) hydrogen bonds : bond 0.03457 / 2.43 ( 226) hydrogen bonds : angle 5.38430 / 3.88 ( 639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.071 Fit side-chains REVERT: A 70 ARG cc_start: 0.7902 (mtt180) cc_final: 0.6752 (ptt90) REVERT: A 117 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6770 (mm) REVERT: A 276 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8059 (tmt-80) outliers start: 12 outliers final: 3 residues processed: 75 average time/residue: 0.5816 time to fit residues: 44.4916 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 214 HIS B 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111872 restraints weight = 4038.449| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.27 r_work: 0.3246 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3351 Z= 0.190 Angle : 0.546 5.447 4543 Z= 0.280 Chirality : 0.042 0.143 506 Planarity : 0.005 0.050 566 Dihedral : 9.670 59.557 497 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 17.16 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.40), residues: 410 helix: 2.73 (0.31), residues: 221 sheet: -0.39 (0.66), residues: 54 loop : 0.72 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.018 0.001 TYR A 157 PHE 0.017 0.002 PHE A 17 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 3350) covalent geometry : angle 0.54499 / 0.28 ( 4541) SS BOND : bond 0.00350 / 0.18 ( 1) SS BOND : angle 1.66366 / 0.96 ( 2) hydrogen bonds : bond 0.03786 / 2.65 ( 226) hydrogen bonds : angle 5.57942 / 4.03 ( 639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.097 Fit side-chains REVERT: A 70 ARG cc_start: 0.7924 (mtt180) cc_final: 0.6865 (ptt90) REVERT: A 91 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.6385 (tmm-80) REVERT: A 115 LYS cc_start: 0.7173 (mttp) cc_final: 0.6778 (mtmt) REVERT: A 117 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6760 (mm) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.6343 time to fit residues: 45.2882 Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.134254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114469 restraints weight = 4013.810| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.26 r_work: 0.3281 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3351 Z= 0.122 Angle : 0.471 5.378 4543 Z= 0.244 Chirality : 0.039 0.136 506 Planarity : 0.005 0.047 566 Dihedral : 9.316 59.874 497 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 17.75 % Favored : 79.59 % 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: 2.68 (0.40), residues: 410 helix: 2.96 (0.32), residues: 221 sheet: -0.32 (0.65), residues: 54 loop : 0.76 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.012 0.001 TYR A 157 PHE 0.014 0.001 PHE A 17 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 3350) covalent geometry : angle 0.47063 / 0.24 ( 4541) SS BOND : bond 0.00176 / 0.09 ( 1) SS BOND : angle 1.05693 / 0.62 ( 2) hydrogen bonds : bond 0.03290 / 2.30 ( 226) hydrogen bonds : angle 5.23387 / 3.79 ( 639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.093 Fit side-chains REVERT: A 70 ARG cc_start: 0.7851 (mtt180) cc_final: 0.6897 (ptt90) REVERT: A 115 LYS cc_start: 0.7136 (mttp) cc_final: 0.6727 (mtmt) REVERT: A 167 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: A 276 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8002 (tmt-80) REVERT: B 52 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8713 (tm-30) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.5159 time to fit residues: 38.5062 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111362 restraints weight = 3884.277| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.23 r_work: 0.3191 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3351 Z= 0.131 Angle : 0.479 5.372 4543 Z= 0.248 Chirality : 0.039 0.135 506 Planarity : 0.005 0.045 566 Dihedral : 9.237 59.628 497 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.25 % Allowed : 18.05 % Favored : 78.70 % 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: 2.72 (0.40), residues: 410 helix: 2.96 (0.31), residues: 221 sheet: -0.26 (0.65), residues: 54 loop : 0.81 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 293 TYR 0.013 0.001 TYR A 157 PHE 0.008 0.001 PHE A 128 TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 3350) covalent geometry : angle 0.47883 / 0.25 ( 4541) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 1.16726 / 0.67 ( 2) hydrogen bonds : bond 0.03349 / 2.33 ( 226) hydrogen bonds : angle 5.21539 / 3.78 ( 639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.081 Fit side-chains REVERT: A 70 ARG cc_start: 0.7837 (mtt180) cc_final: 0.6712 (ptt90) REVERT: A 115 LYS cc_start: 0.6980 (mttp) cc_final: 0.6578 (mtmt) REVERT: A 167 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: A 276 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7954 (tmt-80) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.5986 time to fit residues: 42.8432 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 0.0070 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114145 restraints weight = 3982.411| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.29 r_work: 0.3229 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 3351 Z= 0.101 Angle : 0.449 5.309 4543 Z= 0.233 Chirality : 0.038 0.132 506 Planarity : 0.005 0.044 566 Dihedral : 8.887 57.863 497 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.96 % Allowed : 19.23 % Favored : 77.81 % 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: 2.93 (0.40), residues: 410 helix: 3.13 (0.32), residues: 221 sheet: 0.09 (0.67), residues: 54 loop : 0.79 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 293 TYR 0.008 0.001 TYR A 157 PHE 0.007 0.001 PHE B 27 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 3350) covalent geometry : angle 0.44920 / 0.23 ( 4541) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.82221 / 0.48 ( 2) hydrogen bonds : bond 0.03010 / 2.10 ( 226) hydrogen bonds : angle 4.96651 / 3.62 ( 639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.112 Fit side-chains REVERT: A 70 ARG cc_start: 0.7841 (mtt180) cc_final: 0.6687 (ptt90) REVERT: A 115 LYS cc_start: 0.7003 (mttp) cc_final: 0.6591 (mtmt) REVERT: A 157 TYR cc_start: 0.8040 (m-80) cc_final: 0.6466 (t80) REVERT: A 276 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7956 (tmt-80) REVERT: B 52 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8592 (tm-30) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 0.5259 time to fit residues: 38.7421 Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 214 HIS B 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110289 restraints weight = 3971.627| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.26 r_work: 0.3177 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3351 Z= 0.159 Angle : 0.509 5.371 4543 Z= 0.262 Chirality : 0.040 0.134 506 Planarity : 0.005 0.045 566 Dihedral : 9.213 58.571 497 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 19.82 % Favored : 77.81 % 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: 2.77 (0.39), residues: 410 helix: 2.95 (0.31), residues: 221 sheet: 0.06 (0.68), residues: 54 loop : 0.79 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 293 TYR 0.016 0.001 TYR A 157 PHE 0.010 0.002 PHE A 128 TRP 0.008 0.001 TRP B 57 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3350) covalent geometry : angle 0.50793 / 0.26 ( 4541) SS BOND : bond 0.00277 / 0.15 ( 1) SS BOND : angle 1.42634 / 0.82 ( 2) hydrogen bonds : bond 0.03523 / 2.45 ( 226) hydrogen bonds : angle 5.28350 / 3.83 ( 639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.115 Fit side-chains REVERT: A 70 ARG cc_start: 0.7871 (mtt180) cc_final: 0.6631 (ptt90) REVERT: A 115 LYS cc_start: 0.6977 (mttp) cc_final: 0.6548 (mtmt) REVERT: A 117 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6555 (mm) REVERT: A 276 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8029 (tmt-80) outliers start: 8 outliers final: 3 residues processed: 68 average time/residue: 0.5714 time to fit residues: 39.6787 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 214 HIS B 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.132633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112015 restraints weight = 3945.735| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.30 r_work: 0.3201 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3351 Z= 0.119 Angle : 0.469 5.336 4543 Z= 0.242 Chirality : 0.039 0.130 506 Planarity : 0.005 0.045 566 Dihedral : 9.003 58.824 497 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 19.82 % Favored : 78.11 % 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: 2.88 (0.39), residues: 410 helix: 3.06 (0.31), residues: 221 sheet: 0.11 (0.67), residues: 54 loop : 0.81 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.012 0.001 TYR A 157 PHE 0.008 0.001 PHE A 17 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3350) covalent geometry : angle 0.46825 / 0.24 ( 4541) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 1.00083 / 0.58 ( 2) hydrogen bonds : bond 0.03201 / 2.22 ( 226) hydrogen bonds : angle 5.08358 / 3.70 ( 639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.114 Fit side-chains REVERT: A 70 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6719 (ptt90) REVERT: A 115 LYS cc_start: 0.7016 (mttp) cc_final: 0.6605 (mtmt) REVERT: A 276 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7970 (tmt-80) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.6034 time to fit residues: 43.1498 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 214 HIS B 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110548 restraints weight = 3903.041| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.28 r_work: 0.3182 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3351 Z= 0.148 Angle : 0.507 6.067 4543 Z= 0.264 Chirality : 0.040 0.132 506 Planarity : 0.005 0.044 566 Dihedral : 9.104 56.705 497 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.78 % Allowed : 20.12 % Favored : 78.11 % 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: 2.77 (0.39), residues: 410 helix: 2.94 (0.31), residues: 221 sheet: 0.11 (0.68), residues: 54 loop : 0.80 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.014 0.001 TYR A 157 PHE 0.016 0.002 PHE A 17 TRP 0.008 0.001 TRP B 57 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3350) covalent geometry : angle 0.50660 / 0.26 ( 4541) SS BOND : bond 0.00208 / 0.11 ( 1) SS BOND : angle 1.25742 / 0.72 ( 2) hydrogen bonds : bond 0.03479 / 2.44 ( 226) hydrogen bonds : angle 5.25663 / 3.83 ( 639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.116 Fit side-chains REVERT: A 70 ARG cc_start: 0.7894 (mtt180) cc_final: 0.6710 (ptt90) REVERT: A 115 LYS cc_start: 0.7009 (mttp) cc_final: 0.6599 (mtmt) REVERT: A 276 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7993 (tmt-80) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.6177 time to fit residues: 42.2947 Evaluate side-chains 70 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 33 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 214 HIS B 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112021 restraints weight = 3987.624| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.29 r_work: 0.3202 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 3351 Z= 0.127 Angle : 0.498 6.370 4543 Z= 0.262 Chirality : 0.039 0.130 506 Planarity : 0.005 0.044 566 Dihedral : 8.968 58.774 497 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 20.71 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.40), residues: 410 helix: 2.98 (0.31), residues: 221 sheet: 0.28 (0.74), residues: 46 loop : 0.64 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.012 0.001 TYR A 157 PHE 0.037 0.002 PHE A 17 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 3350) covalent geometry : angle 0.49805 / 0.26 ( 4541) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 0.98703 / 0.57 ( 2) hydrogen bonds : bond 0.03382 / 2.44 ( 226) hydrogen bonds : angle 5.14044 / 3.74 ( 639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1468.03 seconds wall clock time: 25 minutes 38.88 seconds (1538.88 seconds total)