Starting phenix.real_space_refine on Thu Jul 2 02:08:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.cif" model { file = "/net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8exa_28656/07_2026/8exa_28656.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 139 5.49 5 S 2 5.16 5 C 2984 2.51 5 N 1029 2.21 5 O 1385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5539 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2610 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2163 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 49, 'rna3p_pyr': 42} Link IDs: {'rna2p': 10, 'rna3p': 90} Chain breaks: 2 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 252 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1, ' DT:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Time building chain proxies: 1.25, per 1000 atoms: 0.23 Number of scatterers: 5539 At special positions: 0 Unit cell: (81.4, 86.9, 97.9, 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 2 16.00 P 139 15.00 O 1385 8.00 N 1029 7.00 C 2984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.47 Conformation dependent library (CDL) restraints added in 132.1 milliseconds 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 2 sheets defined 53.7% alpha, 15.2% beta 56 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 14 through 46 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 75 through 96 removed outlier: 3.714A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.628A pdb=" N LEU A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 121 removed outlier: 7.383A pdb=" N ILE A 154 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU A 174 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 156 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209 removed outlier: 4.215A pdb=" N VAL A 200 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A 278 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 192 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL A 321 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A 277 " --> pdb=" O VAL A 321 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.57 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: 923 1.33 - 1.45: 2154 1.45 - 1.57: 2579 1.57 - 1.69: 273 1.69 - 1.80: 3 Bond restraints: 5932 Sorted by residual: bond pdb=" C3' DC C 3 " pdb=" C2' DC C 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.68e+00 bond pdb=" C3' DT C 0 " pdb=" C2' DT C 0 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.34e+00 bond pdb=" C3' DG D -7 " pdb=" O3' DG D -7 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.08e+00 bond pdb=" C3' DG C -5 " pdb=" C2' DG C -5 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.59e+00 bond pdb=" C3' DT D 1 " pdb=" C2' DT D 1 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.72e+00 ... (remaining 5927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 7969 0.99 - 1.97: 548 1.97 - 2.96: 133 2.96 - 3.94: 17 3.94 - 4.93: 6 Bond angle restraints: 8673 Sorted by residual: angle pdb=" O4' DC D -10 " pdb=" C4' DC D -10 " pdb=" C3' DC D -10 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT D 1 " pdb=" C4 DT D 1 " pdb=" O4 DT D 1 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C 0 " pdb=" C4 DT C 0 " pdb=" O4 DT C 0 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT D -17 " pdb=" C4 DT D -17 " pdb=" O4 DT D -17 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 8668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 2928 28.56 - 57.13: 246 57.13 - 85.69: 31 85.69 - 114.25: 1 114.25 - 142.82: 1 Dihedral angle restraints: 3207 sinusoidal: 2218 harmonic: 989 Sorted by residual: dihedral pdb=" C4' DC C 3 " pdb=" C3' DC C 3 " pdb=" O3' DC C 3 " pdb=" P DA C 4 " ideal model delta sinusoidal sigma weight residual 220.00 77.18 142.82 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -119.23 -40.77 1 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA LEU A 136 " pdb=" C LEU A 136 " pdb=" N PRO A 137 " pdb=" CA PRO A 137 " ideal model delta harmonic sigma weight residual -180.00 -164.05 -15.95 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 738 0.031 - 0.061: 215 0.061 - 0.092: 67 0.092 - 0.122: 32 0.122 - 0.153: 10 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C3' DA D -4 " pdb=" C4' DA D -4 " pdb=" O3' DA D -4 " pdb=" C2' DA D -4 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" C3' DG D -7 " pdb=" C4' DG D -7 " pdb=" O3' DG D -7 " pdb=" C2' DG D -7 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1059 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.031 2.00e-02 2.50e+03 1.28e-02 4.95e+00 pdb=" N9 G B 3 " 0.028 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 3 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 9 " 0.026 2.00e-02 2.50e+03 1.39e-02 4.35e+00 pdb=" N1 U B 9 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 9 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 9 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U B 9 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 9 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 2 " -0.023 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A B 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A B 2 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 2 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 2 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 2 " 0.003 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 899 2.76 - 3.29: 5072 3.29 - 3.83: 11101 3.83 - 4.36: 12729 4.36 - 4.90: 18341 Nonbonded interactions: 48142 Sorted by model distance: nonbonded pdb=" OG SER A 117 " pdb=" OP1 U B 4 " model vdw 2.223 3.040 nonbonded pdb=" O2 C B-107 " pdb=" N2 G B -6 " model vdw 2.251 3.120 nonbonded pdb=" NH1 ARG A 39 " pdb=" OE1 GLU A 87 " model vdw 2.275 3.120 nonbonded pdb=" N2 G B-114 " pdb=" O4 U B -89 " model vdw 2.301 3.120 nonbonded pdb=" NH1 ARG A 110 " pdb=" OP1 C B 5 " model vdw 2.319 3.120 ... (remaining 48137 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: 0.600 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 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 : 0.004 0.035 5932 Z= 0.309 Angle : 0.590 4.927 8673 Z= 0.398 Chirality : 0.037 0.153 1062 Planarity : 0.003 0.023 596 Dihedral : 17.594 142.816 2571 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.40 % Allowed : 8.50 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.47), residues: 337 helix: 1.86 (0.40), residues: 175 sheet: -1.83 (0.63), residues: 65 loop : -1.41 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.024 0.002 TYR A 309 PHE 0.018 0.002 PHE A 35 TRP 0.006 0.001 TRP A 300 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.31 ( 5932) covalent geometry : angle 0.59012 / 0.40 ( 8673) hydrogen bonds : bond 0.08927 / 6.37 ( 310) hydrogen bonds : angle 3.99413 / 3.04 ( 727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9058 (mt) cc_final: 0.8835 (mt) REVERT: A 95 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7187 (mtm110) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.0890 time to fit residues: 5.3228 Evaluate side-chains 39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 227 GLN A 250 HIS A 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.197300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157548 restraints weight = 7567.024| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.58 r_work: 0.3832 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5932 Z= 0.173 Angle : 0.559 5.501 8673 Z= 0.300 Chirality : 0.035 0.180 1062 Planarity : 0.004 0.025 596 Dihedral : 18.397 145.531 1989 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.64 % Allowed : 9.31 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.48), residues: 337 helix: 2.35 (0.39), residues: 169 sheet: -2.10 (0.61), residues: 72 loop : -1.16 (0.61), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 110 TYR 0.022 0.002 TYR A 309 PHE 0.035 0.003 PHE A 35 TRP 0.007 0.002 TRP A 70 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 5932) covalent geometry : angle 0.55898 / 0.30 ( 8673) hydrogen bonds : bond 0.05341 / 3.63 ( 310) hydrogen bonds : angle 3.48676 / 2.68 ( 727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 143 LYS cc_start: 0.7076 (tttt) cc_final: 0.6525 (mtmt) REVERT: A 214 TYR cc_start: 0.7273 (m-80) cc_final: 0.6840 (m-80) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.0777 time to fit residues: 4.6995 Evaluate side-chains 39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 222 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.191206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150434 restraints weight = 7524.463| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.66 r_work: 0.3765 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 5932 Z= 0.321 Angle : 0.729 7.797 8673 Z= 0.376 Chirality : 0.042 0.166 1062 Planarity : 0.005 0.033 596 Dihedral : 18.589 145.621 1989 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.05 % Allowed : 11.74 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.47), residues: 337 helix: 1.31 (0.38), residues: 176 sheet: -2.02 (0.64), residues: 71 loop : -1.46 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 110 TYR 0.031 0.003 TYR A 309 PHE 0.029 0.003 PHE A 35 TRP 0.010 0.002 TRP A 300 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.32 ( 5932) covalent geometry : angle 0.72883 / 0.38 ( 8673) hydrogen bonds : bond 0.06824 / 4.63 ( 310) hydrogen bonds : angle 3.86187 / 2.99 ( 727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 143 LYS cc_start: 0.7250 (tttt) cc_final: 0.6626 (mtmt) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.0892 time to fit residues: 5.2674 Evaluate side-chains 44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 366 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 0 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.196715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156587 restraints weight = 7364.720| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.60 r_work: 0.3837 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5932 Z= 0.137 Angle : 0.544 6.078 8673 Z= 0.292 Chirality : 0.034 0.184 1062 Planarity : 0.003 0.025 596 Dihedral : 18.405 145.512 1989 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 13.36 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.48), residues: 337 helix: 2.27 (0.39), residues: 169 sheet: -1.72 (0.67), residues: 66 loop : -1.48 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 95 TYR 0.019 0.002 TYR A 309 PHE 0.026 0.002 PHE A 35 TRP 0.009 0.002 TRP A 300 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 ( 5932) covalent geometry : angle 0.54394 / 0.29 ( 8673) hydrogen bonds : bond 0.05087 / 3.39 ( 310) hydrogen bonds : angle 3.43179 / 2.62 ( 727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5273 (OUTLIER) cc_final: 0.4992 (tp) REVERT: A 143 LYS cc_start: 0.7233 (tttt) cc_final: 0.6571 (mtmt) REVERT: A 255 ASN cc_start: 0.7551 (m-40) cc_final: 0.7226 (m110) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.0805 time to fit residues: 4.7548 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 366 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.194082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153604 restraints weight = 7575.868| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.61 r_work: 0.3803 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5932 Z= 0.210 Angle : 0.592 6.824 8673 Z= 0.312 Chirality : 0.036 0.175 1062 Planarity : 0.004 0.027 596 Dihedral : 18.427 146.105 1989 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.26 % Allowed : 12.15 % Favored : 82.59 % 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: 0.37 (0.48), residues: 337 helix: 2.15 (0.39), residues: 169 sheet: -1.99 (0.64), residues: 71 loop : -1.33 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.026 0.002 TYR A 309 PHE 0.024 0.003 PHE A 94 TRP 0.008 0.002 TRP A 300 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 ( 5932) covalent geometry : angle 0.59221 / 0.31 ( 8673) hydrogen bonds : bond 0.05540 / 3.72 ( 310) hydrogen bonds : angle 3.50946 / 2.69 ( 727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5344 (OUTLIER) cc_final: 0.5053 (tp) REVERT: A 143 LYS cc_start: 0.7254 (tttt) cc_final: 0.6619 (mtmt) REVERT: A 214 TYR cc_start: 0.7337 (m-80) cc_final: 0.6932 (m-80) REVERT: A 368 ILE cc_start: 0.5931 (OUTLIER) cc_final: 0.5566 (mt) outliers start: 13 outliers final: 7 residues processed: 46 average time/residue: 0.0927 time to fit residues: 5.4195 Evaluate side-chains 43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.195252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155031 restraints weight = 7448.640| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.61 r_work: 0.3823 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5932 Z= 0.171 Angle : 0.557 5.800 8673 Z= 0.297 Chirality : 0.035 0.180 1062 Planarity : 0.004 0.028 596 Dihedral : 18.402 145.721 1989 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.05 % Allowed : 13.36 % Favored : 82.59 % 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: 0.48 (0.48), residues: 337 helix: 2.27 (0.39), residues: 169 sheet: -2.04 (0.64), residues: 71 loop : -1.28 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 95 TYR 0.023 0.002 TYR A 309 PHE 0.026 0.002 PHE A 35 TRP 0.009 0.002 TRP A 300 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 5932) covalent geometry : angle 0.55699 / 0.30 ( 8673) hydrogen bonds : bond 0.05213 / 3.49 ( 310) hydrogen bonds : angle 3.41299 / 2.61 ( 727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5296 (OUTLIER) cc_final: 0.5009 (tp) REVERT: A 143 LYS cc_start: 0.7269 (tttt) cc_final: 0.6593 (mtmt) REVERT: A 214 TYR cc_start: 0.7325 (m-80) cc_final: 0.6933 (m-80) REVERT: A 255 ASN cc_start: 0.7544 (m-40) cc_final: 0.7152 (m110) REVERT: A 368 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5611 (mt) outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 0.1027 time to fit residues: 5.3662 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.198229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158308 restraints weight = 7464.490| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.63 r_work: 0.3859 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5932 Z= 0.125 Angle : 0.502 4.661 8673 Z= 0.272 Chirality : 0.033 0.186 1062 Planarity : 0.003 0.028 596 Dihedral : 18.315 145.295 1989 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.43 % Allowed : 14.57 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.49), residues: 337 helix: 2.60 (0.39), residues: 167 sheet: -1.65 (0.67), residues: 66 loop : -1.13 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.019 0.002 TYR A 309 PHE 0.022 0.002 PHE A 35 TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 ( 5932) covalent geometry : angle 0.50207 / 0.27 ( 8673) hydrogen bonds : bond 0.04684 / 3.14 ( 310) hydrogen bonds : angle 3.22277 / 2.45 ( 727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5171 (OUTLIER) cc_final: 0.4886 (tp) REVERT: A 143 LYS cc_start: 0.7214 (tttt) cc_final: 0.6564 (mtmt) REVERT: A 255 ASN cc_start: 0.7411 (m-40) cc_final: 0.7151 (m110) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.0938 time to fit residues: 4.8887 Evaluate side-chains 40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 0.0170 chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.7424 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.191625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151644 restraints weight = 7478.837| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.61 r_work: 0.3783 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5932 Z= 0.302 Angle : 0.681 7.691 8673 Z= 0.354 Chirality : 0.040 0.181 1062 Planarity : 0.005 0.041 596 Dihedral : 18.539 145.394 1989 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.45 % Allowed : 12.96 % Favored : 82.59 % 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: -0.05 (0.47), residues: 337 helix: 1.55 (0.38), residues: 176 sheet: -1.80 (0.67), residues: 67 loop : -1.64 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 95 TYR 0.031 0.003 TYR A 309 PHE 0.024 0.003 PHE A 35 TRP 0.008 0.002 TRP A 300 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.30 ( 5932) covalent geometry : angle 0.68149 / 0.35 ( 8673) hydrogen bonds : bond 0.06335 / 4.28 ( 310) hydrogen bonds : angle 3.64519 / 2.80 ( 727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5392 (OUTLIER) cc_final: 0.5070 (tp) REVERT: A 143 LYS cc_start: 0.7217 (tttt) cc_final: 0.6611 (mtmt) REVERT: A 255 ASN cc_start: 0.7301 (m-40) cc_final: 0.7021 (m110) REVERT: A 368 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5667 (mt) outliers start: 11 outliers final: 5 residues processed: 44 average time/residue: 0.1018 time to fit residues: 5.6312 Evaluate side-chains 41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.196570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156679 restraints weight = 7454.707| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.61 r_work: 0.3841 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5932 Z= 0.139 Angle : 0.550 9.172 8673 Z= 0.292 Chirality : 0.034 0.182 1062 Planarity : 0.004 0.038 596 Dihedral : 18.401 146.430 1989 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 14.57 % 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: 0.42 (0.48), residues: 337 helix: 2.03 (0.39), residues: 176 sheet: -1.72 (0.67), residues: 66 loop : -1.52 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 95 TYR 0.036 0.002 TYR A 214 PHE 0.026 0.002 PHE A 35 TRP 0.010 0.002 TRP A 300 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 5932) covalent geometry : angle 0.55043 / 0.29 ( 8673) hydrogen bonds : bond 0.04954 / 3.30 ( 310) hydrogen bonds : angle 3.32532 / 2.53 ( 727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5262 (OUTLIER) cc_final: 0.4988 (tp) REVERT: A 143 LYS cc_start: 0.7194 (tttt) cc_final: 0.6549 (mtmt) REVERT: A 368 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5602 (mt) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.1092 time to fit residues: 6.2961 Evaluate side-chains 41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 16 optimal weight: 0.0010 overall best weight: 0.9708 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.197567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157819 restraints weight = 7579.064| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.58 r_work: 0.3841 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5932 Z= 0.151 Angle : 0.537 5.310 8673 Z= 0.289 Chirality : 0.034 0.185 1062 Planarity : 0.004 0.035 596 Dihedral : 18.374 145.251 1989 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.83 % Allowed : 14.98 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.48), residues: 337 helix: 2.06 (0.39), residues: 174 sheet: -1.68 (0.68), residues: 66 loop : -1.27 (0.62), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 95 TYR 0.033 0.002 TYR A 214 PHE 0.023 0.002 PHE A 35 TRP 0.009 0.002 TRP A 300 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 5932) covalent geometry : angle 0.53657 / 0.29 ( 8673) hydrogen bonds : bond 0.04972 / 3.31 ( 310) hydrogen bonds : angle 3.31736 / 2.54 ( 727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5279 (OUTLIER) cc_final: 0.4999 (tp) REVERT: A 143 LYS cc_start: 0.7192 (tttt) cc_final: 0.6577 (mtmt) REVERT: A 368 ILE cc_start: 0.5955 (OUTLIER) cc_final: 0.5586 (mt) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.1082 time to fit residues: 6.0126 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.197905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.158161 restraints weight = 7474.153| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.61 r_work: 0.3858 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5932 Z= 0.133 Angle : 0.527 6.420 8673 Z= 0.285 Chirality : 0.033 0.188 1062 Planarity : 0.004 0.035 596 Dihedral : 18.330 145.291 1989 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.43 % Allowed : 15.79 % 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: 0.87 (0.49), residues: 337 helix: 2.56 (0.39), residues: 167 sheet: -1.62 (0.68), residues: 66 loop : -1.22 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.025 0.002 TYR A 214 PHE 0.022 0.002 PHE A 35 TRP 0.010 0.002 TRP A 300 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 5932) covalent geometry : angle 0.52690 / 0.29 ( 8673) hydrogen bonds : bond 0.04797 / 3.21 ( 310) hydrogen bonds : angle 3.25152 / 2.48 ( 727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.84 seconds wall clock time: 20 minutes 41.67 seconds (1241.67 seconds total)