Starting phenix.real_space_refine on Thu Jul 2 01:17:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j09_61051/07_2026/9j09_61051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j09_61051/07_2026/9j09_61051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2026/9j09_61051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2026/9j09_61051.map" model { file = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2026/9j09_61051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2026/9j09_61051_neut.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 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 149 5.49 5 S 2 5.16 5 C 2735 2.51 5 N 971 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5227 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2053 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 247} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "R" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2440 Classifications: {'RNA': 114} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 1, 'rna3p_pur': 58, 'rna3p_pyr': 48} Link IDs: {'rna2p': 7, 'rna3p': 106} Chain breaks: 4 Time building chain proxies: 1.04, per 1000 atoms: 0.20 Number of scatterers: 5227 At special positions: 0 Unit cell: (87.36, 97.92, 90.24, 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 149 15.00 O 1370 8.00 N 971 7.00 C 2735 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: 0.33 Conformation dependent library (CDL) restraints added in 63.3 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 484 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 2 sheets defined 51.4% alpha, 12.5% beta 46 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 22 through 63 removed outlier: 3.865A pdb=" N ALA A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 80 removed outlier: 4.150A pdb=" N LYS A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 6.906A pdb=" N ARG A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.717A pdb=" N GLU A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.713A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 161 removed outlier: 3.746A pdb=" N GLY A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 233 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.709A pdb=" N ARG A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG A 253 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR A 259 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 251 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 261 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 249 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 263 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 265 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 245 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 104 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 553 1.32 - 1.44: 2385 1.44 - 1.56: 2417 1.56 - 1.68: 292 1.68 - 1.80: 4 Bond restraints: 5651 Sorted by residual: bond pdb=" P DC C 6 " pdb=" O5' DC C 6 " ideal model delta sigma weight residual 1.593 1.633 -0.040 1.00e-02 1.00e+04 1.62e+01 bond pdb=" C ILE A 227 " pdb=" O ILE A 227 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.05e-02 9.07e+03 1.34e+01 bond pdb=" C3' DG C 11 " pdb=" C2' DG C 11 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DT C 19 " pdb=" C2' DT C 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC C 21 " pdb=" C2' DC C 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 ... (remaining 5646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 8139 4.13 - 8.26: 199 8.26 - 12.40: 9 12.40 - 16.53: 2 16.53 - 20.66: 1 Bond angle restraints: 8350 Sorted by residual: angle pdb=" O3' U R 4 " pdb=" P C R 5 " pdb=" O5' C R 5 " ideal model delta sigma weight residual 104.00 124.66 -20.66 1.50e+00 4.44e-01 1.90e+02 angle pdb=" O4' DG C 27 " pdb=" C1' DG C 27 " pdb=" N9 DG C 27 " ideal model delta sigma weight residual 108.00 113.94 -5.94 7.00e-01 2.04e+00 7.21e+01 angle pdb=" O4' C R 0 " pdb=" C1' C R 0 " pdb=" C2' C R 0 " ideal model delta sigma weight residual 105.80 99.15 6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" C3' U R 3 " pdb=" C2' U R 3 " pdb=" O2' U R 3 " ideal model delta sigma weight residual 110.70 120.08 -9.38 1.50e+00 4.44e-01 3.91e+01 angle pdb=" O2' U R 3 " pdb=" C2' U R 3 " pdb=" C1' U R 3 " ideal model delta sigma weight residual 108.40 99.15 9.25 1.50e+00 4.44e-01 3.80e+01 ... (remaining 8345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 2826 33.25 - 66.50: 508 66.50 - 99.75: 52 99.75 - 133.01: 3 133.01 - 166.26: 1 Dihedral angle restraints: 3390 sinusoidal: 2634 harmonic: 756 Sorted by residual: dihedral pdb=" O4' C R -68 " pdb=" C1' C R -68 " pdb=" N1 C R -68 " pdb=" C2 C R -68 " ideal model delta sinusoidal sigma weight residual 200.00 33.74 166.26 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" C5' A R-152 " pdb=" C4' A R-152 " pdb=" C3' A R-152 " pdb=" O3' A R-152 " ideal model delta sinusoidal sigma weight residual 147.00 102.98 44.02 1 8.00e+00 1.56e-02 4.21e+01 dihedral pdb=" O4' G R-145 " pdb=" C2' G R-145 " pdb=" C1' G R-145 " pdb=" C3' G R-145 " ideal model delta sinusoidal sigma weight residual 25.00 -17.70 42.70 1 8.00e+00 1.56e-02 3.98e+01 ... (remaining 3387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 905 0.145 - 0.290: 44 0.290 - 0.434: 7 0.434 - 0.579: 37 0.579 - 0.724: 18 Chirality restraints: 1011 Sorted by residual: chirality pdb=" P DC D -11 " pdb=" OP1 DC D -11 " pdb=" OP2 DC D -11 " pdb=" O5' DC D -11 " both_signs ideal model delta sigma weight residual True 2.34 -3.06 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" P C R 0 " pdb=" OP1 C R 0 " pdb=" OP2 C R 0 " pdb=" O5' C R 0 " both_signs ideal model delta sigma weight residual True 2.41 -3.10 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" P G R 10 " pdb=" OP1 G R 10 " pdb=" OP2 G R 10 " pdb=" O5' G R 10 " both_signs ideal model delta sigma weight residual True 2.41 -3.10 -0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 1008 not shown) Planarity restraints: 519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 27 " -0.052 2.00e-02 2.50e+03 2.14e-02 1.38e+01 pdb=" N9 DG C 27 " 0.046 2.00e-02 2.50e+03 pdb=" C8 DG C 27 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DG C 27 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG C 27 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DG C 27 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG C 27 " -0.013 2.00e-02 2.50e+03 pdb=" N1 DG C 27 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG C 27 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG C 27 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG C 27 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG C 27 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " 0.024 2.00e-02 2.50e+03 1.41e-02 5.95e+00 pdb=" N9 DG C 17 " -0.035 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 4 " -0.029 2.00e-02 2.50e+03 1.48e-02 4.96e+00 pdb=" N1 U R 4 " 0.028 2.00e-02 2.50e+03 pdb=" C2 U R 4 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U R 4 " 0.009 2.00e-02 2.50e+03 pdb=" N3 U R 4 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U R 4 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U R 4 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U R 4 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U R 4 " 0.004 2.00e-02 2.50e+03 ... (remaining 516 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 119 2.61 - 3.18: 4028 3.18 - 3.76: 9633 3.76 - 4.33: 12155 4.33 - 4.90: 17212 Nonbonded interactions: 43147 Sorted by model distance: nonbonded pdb=" O2' A R -55 " pdb=" O4' U R -54 " model vdw 2.040 3.040 nonbonded pdb=" OD2 ASP A 117 " pdb=" OG SER A 119 " model vdw 2.271 3.040 nonbonded pdb=" O2' C R -94 " pdb=" O4 U R -57 " model vdw 2.283 3.040 nonbonded pdb=" O2 U R -41 " pdb=" N2 G R -10 " model vdw 2.335 2.496 nonbonded pdb=" NH1 ARG A 253 " pdb=" O ALA A 255 " model vdw 2.362 3.120 ... (remaining 43142 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.210 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:5.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4675 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 : 0.008 0.047 5651 Z= 0.571 Angle : 1.371 20.659 8350 Z= 0.901 Chirality : 0.146 0.724 1011 Planarity : 0.005 0.050 519 Dihedral : 26.407 166.258 2906 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % Rotamer: Outliers : 4.95 % Allowed : 1.98 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.40 (0.52), residues: 255 helix: 1.25 (0.47), residues: 121 sheet: -0.19 (0.83), residues: 41 loop : -2.42 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 217 TYR 0.015 0.002 TYR A 195 PHE 0.011 0.002 PHE A 156 TRP 0.012 0.001 TRP A 153 HIS 0.015 0.004 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.57 ( 5651) covalent geometry : angle 1.37097 / 0.90 ( 8350) hydrogen bonds : bond 0.18463 / 12.09 ( 216) hydrogen bonds : angle 9.15292 / 6.75 ( 512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.070 Fit side-chains REVERT: A 11 ASN cc_start: 0.7118 (p0) cc_final: 0.6893 (p0) REVERT: A 97 TYR cc_start: 0.5966 (m-80) cc_final: 0.5723 (m-80) REVERT: A 104 ARG cc_start: 0.4942 (ttp80) cc_final: 0.4389 (mtm110) REVERT: A 106 GLU cc_start: 0.4706 (tt0) cc_final: 0.3879 (tp30) REVERT: A 176 LYS cc_start: 0.7044 (mttp) cc_final: 0.6755 (mttp) REVERT: A 181 ARG cc_start: 0.3147 (mtp180) cc_final: 0.1434 (ptp90) REVERT: A 191 LYS cc_start: 0.6689 (tppp) cc_final: 0.4732 (pmtt) outliers start: 10 outliers final: 1 residues processed: 34 average time/residue: 0.5683 time to fit residues: 19.9517 Evaluate side-chains 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 GLN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.263130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.239990 restraints weight = 4463.516| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 0.65 r_work: 0.4358 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5651 Z= 0.281 Angle : 0.875 10.531 8350 Z= 0.515 Chirality : 0.059 0.378 1011 Planarity : 0.009 0.057 519 Dihedral : 27.150 171.768 2435 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.41 % Favored : 90.20 % Rotamer: Outliers : 3.96 % Allowed : 8.91 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.50), residues: 255 helix: 0.86 (0.44), residues: 115 sheet: -1.44 (0.76), residues: 49 loop : -2.75 (0.55), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 210 TYR 0.027 0.004 TYR A 195 PHE 0.014 0.003 PHE A 156 TRP 0.020 0.003 TRP A 153 HIS 0.007 0.002 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.28 ( 5651) covalent geometry : angle 0.87532 / 0.51 ( 8350) hydrogen bonds : bond 0.12386 / 8.53 ( 216) hydrogen bonds : angle 4.87894 / 3.69 ( 512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.070 Fit side-chains REVERT: A 104 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7557 (mtm110) REVERT: A 181 ARG cc_start: 0.5046 (mtp180) cc_final: 0.3584 (ptp90) outliers start: 8 outliers final: 4 residues processed: 25 average time/residue: 0.6599 time to fit residues: 17.0716 Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.257373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.233517 restraints weight = 4384.321| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 0.67 r_work: 0.4280 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5651 Z= 0.289 Angle : 0.819 9.103 8350 Z= 0.497 Chirality : 0.057 0.368 1011 Planarity : 0.009 0.090 519 Dihedral : 26.981 177.901 2435 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % Rotamer: Outliers : 6.44 % Allowed : 11.88 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.48), residues: 255 helix: 0.17 (0.44), residues: 117 sheet: -2.32 (0.73), residues: 45 loop : -2.91 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 181 TYR 0.023 0.003 TYR A 195 PHE 0.016 0.003 PHE A 156 TRP 0.018 0.003 TRP A 153 HIS 0.005 0.002 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.29 ( 5651) covalent geometry : angle 0.81924 / 0.50 ( 8350) hydrogen bonds : bond 0.11401 / 7.60 ( 216) hydrogen bonds : angle 4.86031 / 3.67 ( 512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 16 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5508 (tp) REVERT: A 104 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7633 (mtm110) REVERT: A 133 TRP cc_start: 0.6743 (p-90) cc_final: 0.5523 (p-90) outliers start: 13 outliers final: 5 residues processed: 26 average time/residue: 0.5317 time to fit residues: 14.3495 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.275307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.244082 restraints weight = 4357.408| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 0.91 r_work: 0.4309 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5651 Z= 0.159 Angle : 0.632 6.336 8350 Z= 0.392 Chirality : 0.046 0.316 1011 Planarity : 0.005 0.036 519 Dihedral : 26.629 177.069 2435 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.06 % Favored : 92.55 % Rotamer: Outliers : 2.97 % Allowed : 15.84 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.50), residues: 255 helix: 1.28 (0.46), residues: 119 sheet: -2.23 (0.73), residues: 45 loop : -2.63 (0.52), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 181 TYR 0.016 0.002 TYR A 195 PHE 0.014 0.002 PHE A 156 TRP 0.011 0.001 TRP A 153 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 ( 5651) covalent geometry : angle 0.63201 / 0.39 ( 8350) hydrogen bonds : bond 0.08077 / 5.55 ( 216) hydrogen bonds : angle 4.27038 / 3.27 ( 512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7459 (mtm110) outliers start: 6 outliers final: 4 residues processed: 19 average time/residue: 0.5200 time to fit residues: 10.2745 Evaluate side-chains 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.269762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.234395 restraints weight = 4384.117| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 1.07 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5651 Z= 0.222 Angle : 0.690 7.206 8350 Z= 0.423 Chirality : 0.049 0.359 1011 Planarity : 0.007 0.051 519 Dihedral : 26.606 179.639 2435 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.41 % Favored : 90.20 % Rotamer: Outliers : 4.95 % Allowed : 16.34 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.50), residues: 255 helix: 1.11 (0.45), residues: 117 sheet: -1.80 (0.73), residues: 49 loop : -2.78 (0.53), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 181 TYR 0.021 0.003 TYR A 195 PHE 0.015 0.002 PHE A 156 TRP 0.015 0.002 TRP A 153 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 ( 5651) covalent geometry : angle 0.69043 / 0.42 ( 8350) hydrogen bonds : bond 0.09693 / 6.42 ( 216) hydrogen bonds : angle 4.39767 / 3.36 ( 512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 15 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5558 (tp) REVERT: A 104 ARG cc_start: 0.8402 (ttp80) cc_final: 0.7724 (mtm110) outliers start: 10 outliers final: 6 residues processed: 24 average time/residue: 0.5434 time to fit residues: 13.5962 Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.274094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.235099 restraints weight = 4350.999| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 1.02 r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5651 Z= 0.162 Angle : 0.609 6.541 8350 Z= 0.378 Chirality : 0.044 0.311 1011 Planarity : 0.005 0.038 519 Dihedral : 26.392 176.349 2435 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.06 % Favored : 92.55 % Rotamer: Outliers : 2.97 % Allowed : 18.81 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.65 (0.52), residues: 255 helix: 1.63 (0.47), residues: 117 sheet: -1.69 (0.75), residues: 49 loop : -2.56 (0.54), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 181 TYR 0.016 0.002 TYR A 195 PHE 0.013 0.002 PHE A 156 TRP 0.012 0.002 TRP A 153 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 ( 5651) covalent geometry : angle 0.60905 / 0.38 ( 8350) hydrogen bonds : bond 0.07610 / 5.12 ( 216) hydrogen bonds : angle 4.14853 / 3.18 ( 512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.068 Fit side-chains REVERT: A 48 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5659 (tp) REVERT: A 104 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7721 (mtm110) outliers start: 6 outliers final: 3 residues processed: 20 average time/residue: 0.5502 time to fit residues: 11.5071 Evaluate side-chains 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.271325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.228313 restraints weight = 4330.359| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 1.17 r_work: 0.4055 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5651 Z= 0.185 Angle : 0.634 6.352 8350 Z= 0.389 Chirality : 0.045 0.342 1011 Planarity : 0.006 0.039 519 Dihedral : 26.282 176.900 2435 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.80 % Favored : 89.80 % Rotamer: Outliers : 3.47 % Allowed : 18.32 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.75 (0.52), residues: 255 helix: 1.55 (0.47), residues: 117 sheet: -1.77 (0.75), residues: 49 loop : -2.58 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.019 0.002 TYR A 195 PHE 0.014 0.002 PHE A 156 TRP 0.012 0.002 TRP A 153 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.19 ( 5651) covalent geometry : angle 0.63399 / 0.39 ( 8350) hydrogen bonds : bond 0.08525 / 5.64 ( 216) hydrogen bonds : angle 4.18989 / 3.20 ( 512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.071 Fit side-chains REVERT: A 48 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5836 (tp) REVERT: A 104 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7428 (mtm110) REVERT: A 227 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7015 (mp) outliers start: 7 outliers final: 4 residues processed: 22 average time/residue: 0.5712 time to fit residues: 13.0974 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.268360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.225238 restraints weight = 4299.138| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 1.17 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5651 Z= 0.205 Angle : 0.676 7.391 8350 Z= 0.409 Chirality : 0.046 0.349 1011 Planarity : 0.007 0.046 519 Dihedral : 26.211 175.539 2435 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.63 % Favored : 90.98 % Rotamer: Outliers : 4.95 % Allowed : 17.33 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.92 (0.52), residues: 255 helix: 1.33 (0.47), residues: 117 sheet: -1.89 (0.75), residues: 49 loop : -2.50 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 181 TYR 0.021 0.002 TYR A 195 PHE 0.014 0.002 PHE A 156 TRP 0.013 0.002 TRP A 153 HIS 0.007 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.21 ( 5651) covalent geometry : angle 0.67568 / 0.41 ( 8350) hydrogen bonds : bond 0.08740 / 5.75 ( 216) hydrogen bonds : angle 4.26025 / 3.24 ( 512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.084 Fit side-chains REVERT: A 48 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5619 (tp) REVERT: A 104 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7666 (mtm110) REVERT: A 131 ASN cc_start: 0.7356 (m-40) cc_final: 0.7096 (m-40) REVERT: A 133 TRP cc_start: 0.6745 (p-90) cc_final: 0.5682 (p-90) REVERT: A 227 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7014 (mp) outliers start: 10 outliers final: 5 residues processed: 25 average time/residue: 0.5878 time to fit residues: 15.3677 Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 25 GLN A 139 GLN A 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.271468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.235186 restraints weight = 4322.861| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 1.07 r_work: 0.4229 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5651 Z= 0.155 Angle : 0.603 6.692 8350 Z= 0.371 Chirality : 0.042 0.313 1011 Planarity : 0.005 0.037 519 Dihedral : 26.120 173.498 2435 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.02 % Favored : 90.59 % Rotamer: Outliers : 3.96 % Allowed : 17.33 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.52 (0.53), residues: 255 helix: 1.82 (0.48), residues: 117 sheet: -1.81 (0.75), residues: 49 loop : -2.48 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.016 0.002 TYR A 195 PHE 0.014 0.001 PHE A 156 TRP 0.011 0.002 TRP A 153 HIS 0.008 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 ( 5651) covalent geometry : angle 0.60268 / 0.37 ( 8350) hydrogen bonds : bond 0.07346 / 4.88 ( 216) hydrogen bonds : angle 4.10307 / 3.13 ( 512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.072 Fit side-chains REVERT: A 48 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.6089 (tp) REVERT: A 49 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6456 (mp0) REVERT: A 104 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7608 (mtm110) REVERT: A 131 ASN cc_start: 0.7644 (m-40) cc_final: 0.7033 (m-40) REVERT: A 133 TRP cc_start: 0.6738 (p-90) cc_final: 0.5621 (p-90) outliers start: 8 outliers final: 5 residues processed: 24 average time/residue: 0.5174 time to fit residues: 13.0140 Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.267707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.233792 restraints weight = 4355.179| |-----------------------------------------------------------------------------| r_work (start): 0.4697 rms_B_bonded: 1.00 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5651 Z= 0.214 Angle : 0.678 7.358 8350 Z= 0.409 Chirality : 0.047 0.356 1011 Planarity : 0.007 0.051 519 Dihedral : 26.139 174.597 2433 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.80 % Favored : 89.80 % Rotamer: Outliers : 3.47 % Allowed : 17.33 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.94 (0.52), residues: 255 helix: 1.32 (0.47), residues: 117 sheet: -1.94 (0.74), residues: 49 loop : -2.51 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 181 TYR 0.020 0.002 TYR A 195 PHE 0.015 0.002 PHE A 156 TRP 0.014 0.002 TRP A 153 HIS 0.005 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 ( 5651) covalent geometry : angle 0.67789 / 0.41 ( 8350) hydrogen bonds : bond 0.09036 / 5.90 ( 216) hydrogen bonds : angle 4.27492 / 3.25 ( 512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.148 Fit side-chains REVERT: A 48 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5633 (tp) REVERT: A 104 ARG cc_start: 0.8369 (ttp80) cc_final: 0.7725 (mtm110) REVERT: A 131 ASN cc_start: 0.7365 (m-40) cc_final: 0.7056 (m-40) REVERT: A 133 TRP cc_start: 0.6718 (p-90) cc_final: 0.5662 (p-90) outliers start: 7 outliers final: 5 residues processed: 23 average time/residue: 0.5477 time to fit residues: 13.2723 Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 1 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 25 GLN A 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.270674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.238730 restraints weight = 4405.205| |-----------------------------------------------------------------------------| r_work (start): 0.4726 rms_B_bonded: 0.99 r_work (final): 0.4726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5651 Z= 0.155 Angle : 0.606 6.637 8350 Z= 0.372 Chirality : 0.042 0.319 1011 Planarity : 0.005 0.038 519 Dihedral : 26.070 172.841 2433 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.63 % Favored : 90.98 % Rotamer: Outliers : 4.46 % Allowed : 16.34 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.57 (0.53), residues: 255 helix: 1.73 (0.48), residues: 117 sheet: -1.84 (0.75), residues: 49 loop : -2.43 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.017 0.002 TYR A 195 PHE 0.014 0.001 PHE A 156 TRP 0.012 0.001 TRP A 153 HIS 0.006 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 ( 5651) covalent geometry : angle 0.60611 / 0.37 ( 8350) hydrogen bonds : bond 0.07394 / 4.88 ( 216) hydrogen bonds : angle 4.12666 / 3.14 ( 512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1354.14 seconds wall clock time: 23 minutes 53.99 seconds (1433.99 seconds total)