Starting phenix.real_space_refine on Thu Sep 10 23:56:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8exa_28656/09_2026/8exa_28656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8exa_28656/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8exa_28656/09_2026/8exa_28656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8exa_28656/09_2026/8exa_28656.map" model { file = "/net/cci-nas-00/data/ceres_data/8exa_28656/09_2026/8exa_28656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8exa_28656/09_2026/8exa_28656.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8exa_28656/09_2026/8exa_28656.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8exa_28656/09_2026/8exa_28656.cif" } 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-2.2.1-6174/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: {'RNAv2': 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: 1.52, per 1000 atoms: 0.27 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: 0.49 Conformation dependent library (CDL) restraints added in 410.6 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: 0.96 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: 1.46 Time building geometry restraints manager: 0.70 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 - 1.14: 7842 1.14 - 2.28: 524 2.28 - 3.42: 262 3.42 - 4.56: 30 4.56 - 5.71: 15 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: 2803 28.56 - 57.13: 339 57.13 - 85.69: 64 85.69 - 114.25: 0 114.25 - 142.82: 1 Dihedral angle restraints: 3207 sinusoidal: 2218 harmonic: 989 Sorted by residual: dihedral pdb=" C4' A B -76 " pdb=" C3' A B -76 " pdb=" C2' A B -76 " pdb=" C1' A B -76 " ideal model delta sinusoidal sigma weight residual 36.34 -38.11 74.45 1 3.10e+00 1.04e-01 7.31e+02 dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.34 -37.40 73.75 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' C B -39 " pdb=" C3' C B -39 " pdb=" C2' C B -39 " pdb=" C1' C B -39 " ideal model delta sinusoidal sigma weight residual 36.34 -36.12 72.46 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 3204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 856 0.070 - 0.140: 81 0.140 - 0.210: 20 0.210 - 0.280: 101 0.280 - 0.349: 4 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C2' U B 9 " pdb=" C3' U B 9 " pdb=" O2' U B 9 " pdb=" C1' U B 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' A B -76 " pdb=" C4' A B -76 " pdb=" O3' A B -76 " pdb=" C2' A B -76 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (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: 0.800 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.020 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- 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= 0.315 Angle : 0.792 5.706 8673 Z= 0.435 Chirality : 0.088 0.349 1062 Planarity : 0.003 0.023 596 Dihedral : 20.815 142.816 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 0.00448 / 0.32 ( 5932) covalent geometry : angle 0.79208 / 0.43 ( 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 : 0.134 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: 0.0880 time to fit residues: 5.3041 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 : 0.139 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.4391 r_free = 0.4391 target = 0.197011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157409 restraints weight = 7564.848| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.59 r_work: 0.3831 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5932 Z= 0.241 Angle : 1.114 19.880 8673 Z= 0.467 Chirality : 0.098 1.144 1062 Planarity : 0.004 0.024 596 Dihedral : 20.935 144.573 1989 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.64 % Allowed : 8.50 % Favored : 87.85 % 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: 0.62 (0.48), residues: 337 helix: 2.39 (0.39), residues: 169 sheet: -2.02 (0.61), residues: 71 loop : -1.17 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 252 TYR 0.028 0.002 TYR A 309 PHE 0.031 0.002 PHE A 35 TRP 0.008 0.002 TRP A 70 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.24 ( 5932) covalent geometry : angle 1.11378 / 0.47 ( 8673) hydrogen bonds : bond 0.05381 / 3.64 ( 310) hydrogen bonds : angle 3.51439 / 2.69 ( 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 48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.164 Fit side-chains REVERT: A 61 LEU cc_start: 0.8953 (mt) cc_final: 0.8748 (mt) REVERT: A 143 LYS cc_start: 0.7086 (tttt) cc_final: 0.6528 (mtmt) REVERT: A 214 TYR cc_start: 0.7282 (m-80) cc_final: 0.6851 (m-80) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.0835 time to fit residues: 4.9264 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.190732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150601 restraints weight = 7544.578| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.59 r_work: 0.3775 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 5932 Z= 0.320 Angle : 1.054 15.061 8673 Z= 0.455 Chirality : 0.078 1.042 1062 Planarity : 0.005 0.032 596 Dihedral : 20.912 152.019 1989 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.05 % Allowed : 11.34 % Favored : 84.62 % 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: 0.02 (0.47), residues: 337 helix: 1.78 (0.39), residues: 169 sheet: -2.01 (0.64), residues: 71 loop : -1.46 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 95 TYR 0.035 0.003 TYR A 309 PHE 0.029 0.003 PHE A 35 TRP 0.009 0.002 TRP A 300 HIS 0.004 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.32 ( 5932) covalent geometry : angle 1.05355 / 0.46 ( 8673) hydrogen bonds : bond 0.06837 / 4.67 ( 310) hydrogen bonds : angle 3.77258 / 2.92 ( 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 50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.132 Fit side-chains REVERT: A 61 LEU cc_start: 0.8957 (mt) cc_final: 0.8740 (mt) REVERT: A 95 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7143 (mtm110) REVERT: A 143 LYS cc_start: 0.7213 (tttt) cc_final: 0.6605 (mtmt) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.0921 time to fit residues: 5.4734 Evaluate side-chains 46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 0 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.196986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.157274 restraints weight = 7401.526| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.63 r_work: 0.3843 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5932 Z= 0.161 Angle : 0.894 15.491 8673 Z= 0.384 Chirality : 0.068 0.971 1062 Planarity : 0.003 0.025 596 Dihedral : 20.698 150.077 1989 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.83 % Allowed : 13.36 % Favored : 83.81 % 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: 0.69 (0.48), residues: 337 helix: 2.43 (0.39), residues: 169 sheet: -1.70 (0.66), residues: 66 loop : -1.42 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.024 0.002 TYR A 309 PHE 0.025 0.002 PHE A 35 TRP 0.007 0.001 TRP A 300 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 5932) covalent geometry : angle 0.89416 / 0.38 ( 8673) hydrogen bonds : bond 0.05061 / 3.40 ( 310) hydrogen bonds : angle 3.35243 / 2.57 ( 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 45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8909 (mt) cc_final: 0.8701 (mt) REVERT: A 143 LYS cc_start: 0.7199 (tttt) cc_final: 0.6580 (mtmt) REVERT: A 255 ASN cc_start: 0.7678 (m110) cc_final: 0.7177 (m110) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.0824 time to fit residues: 4.7082 Evaluate side-chains 40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.192792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152911 restraints weight = 7600.830| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.61 r_work: 0.3803 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5932 Z= 0.238 Angle : 0.940 13.396 8673 Z= 0.406 Chirality : 0.066 0.756 1062 Planarity : 0.004 0.028 596 Dihedral : 20.673 150.567 1989 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: 0.41 (0.48), residues: 337 helix: 2.14 (0.39), residues: 169 sheet: -1.94 (0.64), residues: 71 loop : -1.27 (0.62), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.032 0.002 TYR A 309 PHE 0.023 0.003 PHE A 35 TRP 0.009 0.002 TRP A 300 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 ( 5932) covalent geometry : angle 0.93965 / 0.41 ( 8673) hydrogen bonds : bond 0.05906 / 4.01 ( 310) hydrogen bonds : angle 3.50870 / 2.71 ( 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 48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5438 (OUTLIER) cc_final: 0.5104 (tp) REVERT: A 61 LEU cc_start: 0.8927 (mt) cc_final: 0.8702 (mt) REVERT: A 143 LYS cc_start: 0.7219 (tttt) cc_final: 0.6597 (mtmt) REVERT: A 255 ASN cc_start: 0.7647 (m110) cc_final: 0.7079 (m110) REVERT: A 368 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5575 (mt) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.0989 time to fit residues: 5.9282 Evaluate side-chains 43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.194935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155453 restraints weight = 7468.426| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.60 r_work: 0.3834 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5932 Z= 0.184 Angle : 0.874 12.486 8673 Z= 0.378 Chirality : 0.063 0.644 1062 Planarity : 0.004 0.028 596 Dihedral : 20.630 149.667 1989 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.64 % Allowed : 14.17 % 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: 0.61 (0.48), residues: 337 helix: 2.37 (0.39), residues: 169 sheet: -1.96 (0.64), residues: 71 loop : -1.21 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 248 TYR 0.025 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 ( 5932) covalent geometry : angle 0.87410 / 0.38 ( 8673) hydrogen bonds : bond 0.05339 / 3.61 ( 310) hydrogen bonds : angle 3.37093 / 2.59 ( 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: 9 poor density : 34 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5288 (OUTLIER) cc_final: 0.4998 (tp) REVERT: A 61 LEU cc_start: 0.8916 (mt) cc_final: 0.8693 (mt) REVERT: A 143 LYS cc_start: 0.7205 (tttt) cc_final: 0.6559 (mtmt) REVERT: A 255 ASN cc_start: 0.7564 (m110) cc_final: 0.7163 (m110) REVERT: A 368 ILE cc_start: 0.5952 (OUTLIER) cc_final: 0.5598 (mt) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.0949 time to fit residues: 5.0255 Evaluate side-chains 42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.194798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155014 restraints weight = 7532.993| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.61 r_work: 0.3826 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1620 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= 0.200 Angle : 0.871 11.336 8673 Z= 0.378 Chirality : 0.062 0.609 1062 Planarity : 0.004 0.035 596 Dihedral : 20.607 149.258 1989 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: 0.60 (0.48), residues: 337 helix: 2.30 (0.39), residues: 169 sheet: -1.66 (0.67), residues: 66 loop : -1.41 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 95 TYR 0.027 0.002 TYR A 309 PHE 0.026 0.002 PHE A 35 TRP 0.008 0.001 TRP A 300 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 ( 5932) covalent geometry : angle 0.87081 / 0.38 ( 8673) hydrogen bonds : bond 0.05551 / 3.77 ( 310) hydrogen bonds : angle 3.38902 / 2.61 ( 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: 9 poor density : 34 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.5027 (tp) REVERT: A 61 LEU cc_start: 0.8918 (mt) cc_final: 0.8683 (mt) REVERT: A 143 LYS cc_start: 0.7199 (tttt) cc_final: 0.6590 (mtmt) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.0879 time to fit residues: 4.7519 Evaluate side-chains 41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.193707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.153870 restraints weight = 7522.960| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.59 r_work: 0.3815 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5932 Z= 0.229 Angle : 0.895 10.031 8673 Z= 0.391 Chirality : 0.063 0.609 1062 Planarity : 0.004 0.029 596 Dihedral : 20.629 148.406 1989 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.45 % Allowed : 13.77 % 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: 0.22 (0.47), residues: 337 helix: 1.78 (0.38), residues: 176 sheet: -1.71 (0.67), residues: 66 loop : -1.52 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 95 TYR 0.028 0.003 TYR A 309 PHE 0.026 0.003 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 0.00482 / 0.23 ( 5932) covalent geometry : angle 0.89499 / 0.39 ( 8673) hydrogen bonds : bond 0.05874 / 4.01 ( 310) hydrogen bonds : angle 3.48771 / 2.70 ( 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 47 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5348 (OUTLIER) cc_final: 0.5027 (tp) REVERT: A 61 LEU cc_start: 0.8945 (mt) cc_final: 0.8722 (mt) REVERT: A 143 LYS cc_start: 0.7193 (tttt) cc_final: 0.6593 (mtmt) REVERT: A 368 ILE cc_start: 0.5990 (OUTLIER) cc_final: 0.5629 (mt) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.0896 time to fit residues: 5.0833 Evaluate side-chains 44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.198387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158478 restraints weight = 7506.053| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.65 r_work: 0.3863 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5932 Z= 0.147 Angle : 0.820 10.044 8673 Z= 0.359 Chirality : 0.059 0.488 1062 Planarity : 0.004 0.031 596 Dihedral : 20.509 148.637 1989 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.64 % Allowed : 15.38 % Favored : 80.97 % 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 (0.48), residues: 337 helix: 2.58 (0.39), residues: 167 sheet: -1.67 (0.67), residues: 66 loop : -1.24 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 95 TYR 0.019 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.009 0.001 TRP A 300 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 5932) covalent geometry : angle 0.82016 / 0.36 ( 8673) hydrogen bonds : bond 0.05162 / 3.49 ( 310) hydrogen bonds : angle 3.25987 / 2.50 ( 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 46 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4957 (tp) REVERT: A 143 LYS cc_start: 0.7196 (tttt) cc_final: 0.6572 (mtmt) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.0826 time to fit residues: 4.7840 Evaluate side-chains 38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.199004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.159046 restraints weight = 7549.773| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.66 r_work: 0.3865 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5932 Z= 0.148 Angle : 0.818 11.482 8673 Z= 0.357 Chirality : 0.058 0.469 1062 Planarity : 0.004 0.037 596 Dihedral : 20.460 148.920 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 : 16.19 % Favored : 80.97 % 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: 0.84 (0.48), residues: 337 helix: 2.52 (0.39), residues: 167 sheet: -1.60 (0.67), residues: 66 loop : -1.23 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 95 TYR 0.021 0.002 TYR A 309 PHE 0.020 0.002 PHE A 35 TRP 0.009 0.001 TRP A 300 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 5932) covalent geometry : angle 0.81810 / 0.36 ( 8673) hydrogen bonds : bond 0.05226 / 3.57 ( 310) hydrogen bonds : angle 3.27935 / 2.49 ( 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 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 Fit side-chains revert: symmetry clash REVERT: A 40 ILE cc_start: 0.5201 (OUTLIER) cc_final: 0.4927 (tp) REVERT: A 143 LYS cc_start: 0.7196 (tttt) cc_final: 0.6561 (mtmt) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.0834 time to fit residues: 4.1642 Evaluate side-chains 39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4420 r_free = 0.4420 target = 0.199129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158934 restraints weight = 7531.948| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.67 r_work: 0.3866 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5932 Z= 0.154 Angle : 0.805 10.261 8673 Z= 0.352 Chirality : 0.057 0.463 1062 Planarity : 0.004 0.034 596 Dihedral : 20.397 149.012 1989 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.43 % Allowed : 16.19 % Favored : 81.38 % 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: 0.80 (0.48), residues: 337 helix: 2.52 (0.39), residues: 167 sheet: -1.63 (0.67), residues: 66 loop : -1.30 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.022 0.002 TYR A 309 PHE 0.022 0.002 PHE A 35 TRP 0.010 0.001 TRP A 300 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 5932) covalent geometry : angle 0.80480 / 0.35 ( 8673) hydrogen bonds : bond 0.05327 / 3.67 ( 310) hydrogen bonds : angle 3.28136 / 2.48 ( 727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1223.85 seconds wall clock time: 21 minutes 51.20 seconds (1311.20 seconds total)