Starting phenix.real_space_refine on Tue Aug 4 16:55:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j09_61051/08_2026/9j09_61051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j09_61051/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j09_61051/08_2026/9j09_61051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j09_61051/08_2026/9j09_61051_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j09_61051/08_2026/9j09_61051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j09_61051/08_2026/9j09_61051.map" } 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-2.2rc3-6140/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: 1.41, per 1000 atoms: 0.27 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: 0.53 Conformation dependent library (CDL) restraints added in 99.9 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: 0.71 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: 0.98 Time building geometry restraints manager: 0.67 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=" P U R -4 " pdb=" O5' U R -4 " ideal model delta sigma weight residual 1.593 1.629 -0.036 1.00e-02 1.00e+04 1.31e+01 bond pdb=" P U R -3 " pdb=" O5' U R -3 " ideal model delta sigma weight residual 1.593 1.629 -0.036 1.00e-02 1.00e+04 1.28e+01 ... (remaining 5646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 8139 4.13 - 8.26: 200 8.26 - 12.40: 8 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 1.90e+00 2.77e-01 1.18e+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=" O3' U R 3 " pdb=" C3' U R 3 " pdb=" C2' U R 3 " ideal model delta sigma weight residual 113.70 122.85 -9.15 1.60e+00 3.91e-01 3.27e+01 angle pdb=" C4' U R 3 " pdb=" C3' U R 3 " pdb=" C2' U R 3 " ideal model delta sigma weight residual 102.60 96.97 5.63 1.00e+00 1.00e+00 3.17e+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: 919 0.145 - 0.290: 30 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: 4.930 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.680 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- 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= 0.603 Angle : 1.414 20.659 8350 Z= 0.955 Chirality : 0.148 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 0.00810 / 0.60 ( 5651) covalent geometry : angle 1.41406 / 0.95 ( 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 : 0.111 Fit side-chains REVERT: A 11 ASN cc_start: 0.7118 (p0) cc_final: 0.6894 (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: 0.6756 (mttp) REVERT: A 181 ARG cc_start: 0.3147 (mtp180) cc_final: 0.1391 (ptp-170) 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: 0.7780 time to fit residues: 27.2561 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 : 0.112 ------------------------------------------------------------------------------- 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: 0.0980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4929 r_free = 0.4929 target = 0.265222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.238725 restraints weight = 4469.765| |-----------------------------------------------------------------------------| r_work (start): 0.4715 rms_B_bonded: 0.74 r_work: 0.4318 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5651 Z= 0.252 Angle : 0.862 12.369 8350 Z= 0.492 Chirality : 0.055 0.360 1011 Planarity : 0.008 0.048 519 Dihedral : 27.045 172.022 2435 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.41 % Favored : 90.20 % Rotamer: Outliers : 3.96 % Allowed : 7.92 % Favored : 88.12 % 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: -0.95 (0.51), residues: 255 helix: 1.17 (0.45), residues: 115 sheet: -1.31 (0.77), residues: 49 loop : -2.62 (0.56), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 210 TYR 0.025 0.003 TYR A 195 PHE 0.013 0.003 PHE A 156 TRP 0.018 0.003 TRP A 153 HIS 0.006 0.002 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.25 ( 5651) covalent geometry : angle 0.86175 / 0.49 ( 8350) hydrogen bonds : bond 0.12260 / 8.48 ( 216) hydrogen bonds : angle 4.79393 / 3.64 ( 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 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.115 Fit side-chains REVERT: A 104 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7515 (mtm110) REVERT: A 181 ARG cc_start: 0.4911 (mtp180) cc_final: 0.3334 (ptp90) outliers start: 8 outliers final: 4 residues processed: 23 average time/residue: 0.8303 time to fit residues: 19.7369 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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: 5.9990 chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4857 r_free = 0.4857 target = 0.255521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.234386 restraints weight = 4370.782| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 0.53 r_work: 0.4343 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 5651 Z= 0.305 Angle : 0.941 10.833 8350 Z= 0.539 Chirality : 0.061 0.393 1011 Planarity : 0.011 0.086 519 Dihedral : 27.035 179.339 2435 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.98 % Favored : 88.24 % Rotamer: Outliers : 5.94 % Allowed : 12.87 % 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: -2.52 (0.47), residues: 255 helix: -0.26 (0.44), residues: 117 sheet: -2.55 (0.72), residues: 45 loop : -2.98 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 181 TYR 0.028 0.004 TYR A 206 PHE 0.017 0.004 PHE A 156 TRP 0.021 0.004 TRP A 153 HIS 0.010 0.003 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.31 ( 5651) covalent geometry : angle 0.94084 / 0.54 ( 8350) hydrogen bonds : bond 0.13207 / 8.79 ( 216) hydrogen bonds : angle 5.09727 / 3.85 ( 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 26 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 14 time to evaluate : 0.084 Fit side-chains REVERT: A 48 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5579 (tp) REVERT: A 109 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6855 (tt0) REVERT: A 133 TRP cc_start: 0.6809 (p-90) cc_final: 0.5539 (p-90) outliers start: 12 outliers final: 4 residues processed: 25 average time/residue: 0.6374 time to fit residues: 16.5494 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 0.0470 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** 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 = 0.5018 r_free = 0.5018 target = 0.273068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.229767 restraints weight = 4333.940| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 1.12 r_work: 0.4110 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3488 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= 0.176 Angle : 0.692 8.620 8350 Z= 0.411 Chirality : 0.046 0.353 1011 Planarity : 0.006 0.039 519 Dihedral : 26.687 176.478 2435 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.63 % Favored : 90.98 % Rotamer: Outliers : 2.97 % Allowed : 17.33 % Favored : 79.70 % 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: -1.49 (0.49), residues: 255 helix: 0.91 (0.45), residues: 117 sheet: -2.30 (0.74), residues: 45 loop : -2.81 (0.50), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 253 TYR 0.017 0.002 TYR A 195 PHE 0.015 0.002 PHE A 156 TRP 0.013 0.002 TRP A 153 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.18 ( 5651) covalent geometry : angle 0.69219 / 0.41 ( 8350) hydrogen bonds : bond 0.08726 / 5.96 ( 216) hydrogen bonds : angle 4.41284 / 3.37 ( 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 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 104 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7289 (mtp85) REVERT: A 106 GLU cc_start: 0.7085 (tt0) cc_final: 0.6739 (tp30) REVERT: A 133 TRP cc_start: 0.6799 (p-90) cc_final: 0.5530 (p-90) outliers start: 6 outliers final: 4 residues processed: 20 average time/residue: 0.5171 time to fit residues: 10.8177 Evaluate side-chains 19 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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: 5.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4999 r_free = 0.4999 target = 0.270427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.233054 restraints weight = 4381.522| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 1.15 r_work: 0.4220 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5651 Z= 0.199 Angle : 0.704 7.627 8350 Z= 0.417 Chirality : 0.047 0.380 1011 Planarity : 0.007 0.046 519 Dihedral : 26.543 178.039 2435 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % Rotamer: Outliers : 2.97 % Allowed : 18.32 % 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: -1.15 (0.51), residues: 255 helix: 1.16 (0.46), residues: 117 sheet: -1.92 (0.72), residues: 49 loop : -2.71 (0.54), 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 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.20 ( 5651) covalent geometry : angle 0.70409 / 0.42 ( 8350) hydrogen bonds : bond 0.09654 / 6.42 ( 216) hydrogen bonds : angle 4.34651 / 3.32 ( 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 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.087 Fit side-chains REVERT: A 48 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5827 (tp) REVERT: A 104 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7516 (mtp85) REVERT: A 106 GLU cc_start: 0.7148 (tt0) cc_final: 0.6812 (tp30) outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 0.5269 time to fit residues: 12.0926 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.066 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.5010 r_free = 0.5010 target = 0.271949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.235521 restraints weight = 4320.926| |-----------------------------------------------------------------------------| r_work (start): 0.4695 rms_B_bonded: 0.98 r_work: 0.4246 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4023 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= 0.179 Angle : 0.659 6.785 8350 Z= 0.392 Chirality : 0.044 0.358 1011 Planarity : 0.006 0.037 519 Dihedral : 26.366 175.494 2435 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.24 % Favored : 91.37 % 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: -0.86 (0.51), residues: 255 helix: 1.36 (0.47), residues: 117 sheet: -1.82 (0.73), residues: 49 loop : -2.48 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 181 TYR 0.018 0.002 TYR A 195 PHE 0.015 0.002 PHE A 156 TRP 0.012 0.002 TRP A 153 HIS 0.006 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.18 ( 5651) covalent geometry : angle 0.65858 / 0.39 ( 8350) hydrogen bonds : bond 0.08276 / 5.53 ( 216) hydrogen bonds : angle 4.22039 / 3.22 ( 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 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.079 Fit side-chains REVERT: A 104 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7494 (mtm110) REVERT: A 106 GLU cc_start: 0.7198 (tt0) cc_final: 0.6932 (tp30) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.4918 time to fit residues: 11.8110 Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** 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 = 0.5013 r_free = 0.5013 target = 0.272197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.229699 restraints weight = 4324.991| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 1.21 r_work: 0.4089 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5651 Z= 0.171 Angle : 0.645 7.137 8350 Z= 0.385 Chirality : 0.043 0.355 1011 Planarity : 0.006 0.037 519 Dihedral : 26.279 174.683 2435 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.41 % Favored : 90.20 % Rotamer: Outliers : 4.46 % Allowed : 17.33 % 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: -0.76 (0.52), residues: 255 helix: 1.54 (0.47), residues: 117 sheet: -1.81 (0.73), residues: 49 loop : -2.55 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 181 TYR 0.017 0.002 TYR A 195 PHE 0.015 0.002 PHE A 156 TRP 0.011 0.002 TRP A 153 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 ( 5651) covalent geometry : angle 0.64497 / 0.39 ( 8350) hydrogen bonds : bond 0.08231 / 5.48 ( 216) hydrogen bonds : angle 4.15737 / 3.18 ( 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 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.110 Fit side-chains REVERT: A 48 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5966 (tp) REVERT: A 104 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7434 (mtm110) REVERT: A 106 GLU cc_start: 0.7162 (tt0) cc_final: 0.6799 (tp30) REVERT: A 131 ASN cc_start: 0.7694 (m-40) cc_final: 0.7260 (m-40) REVERT: A 133 TRP cc_start: 0.6797 (p-90) cc_final: 0.5601 (p-90) outliers start: 9 outliers final: 6 residues processed: 24 average time/residue: 0.4087 time to fit residues: 10.3856 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 : 0.127 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 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 = 0.5000 r_free = 0.5000 target = 0.271274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.254233 restraints weight = 4311.073| |-----------------------------------------------------------------------------| r_work (start): 0.4863 rms_B_bonded: 0.59 r_work: 0.4558 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.4498 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.4468 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= 0.165 Angle : 0.627 7.131 8350 Z= 0.374 Chirality : 0.042 0.346 1011 Planarity : 0.006 0.038 519 Dihedral : 26.167 172.342 2435 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.06 % Favored : 92.55 % 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: -0.54 (0.53), residues: 255 helix: 1.65 (0.48), residues: 117 sheet: -1.76 (0.75), residues: 49 loop : -2.29 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 181 TYR 0.018 0.002 TYR A 195 PHE 0.014 0.002 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 0.00294 / 0.16 ( 5651) covalent geometry : angle 0.62671 / 0.37 ( 8350) hydrogen bonds : bond 0.07521 / 5.01 ( 216) hydrogen bonds : angle 4.12847 / 3.15 ( 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 24 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.079 Fit side-chains REVERT: A 104 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7626 (mtp85) outliers start: 8 outliers final: 6 residues processed: 23 average time/residue: 0.4657 time to fit residues: 11.1549 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 : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR 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: 8.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** 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 = 0.4985 r_free = 0.4985 target = 0.269267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.228669 restraints weight = 4318.139| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 1.15 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5651 Z= 0.187 Angle : 0.668 6.909 8350 Z= 0.394 Chirality : 0.044 0.375 1011 Planarity : 0.007 0.045 519 Dihedral : 26.130 173.478 2435 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % 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: -0.82 (0.52), residues: 255 helix: 1.41 (0.47), residues: 117 sheet: -1.86 (0.74), residues: 49 loop : -2.45 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 181 TYR 0.019 0.002 TYR A 195 PHE 0.015 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 0.00346 / 0.19 ( 5651) covalent geometry : angle 0.66752 / 0.39 ( 8350) hydrogen bonds : bond 0.08601 / 5.66 ( 216) hydrogen bonds : angle 4.21312 / 3.20 ( 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: 9 poor density : 16 time to evaluate : 0.067 Fit side-chains REVERT: A 48 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5613 (tp) REVERT: A 104 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7629 (mtp85) REVERT: A 131 ASN cc_start: 0.7296 (m-40) cc_final: 0.7050 (m-40) REVERT: A 133 TRP cc_start: 0.6695 (p-90) cc_final: 0.5675 (p-90) outliers start: 9 outliers final: 6 residues processed: 24 average time/residue: 0.4345 time to fit residues: 10.9794 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 : 0.107 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 chunk 24 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 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 25 GLN ** 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 = 0.5003 r_free = 0.5003 target = 0.271809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.233790 restraints weight = 4358.692| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 1.04 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.4724 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= 0.156 Angle : 0.618 6.653 8350 Z= 0.369 Chirality : 0.041 0.344 1011 Planarity : 0.006 0.038 519 Dihedral : 26.040 172.388 2435 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.84 % Favored : 91.76 % Rotamer: Outliers : 3.96 % Allowed : 16.83 % 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: -0.56 (0.53), residues: 255 helix: 1.54 (0.47), residues: 119 sheet: -1.77 (0.75), residues: 49 loop : -2.25 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.016 0.002 TYR A 195 PHE 0.013 0.001 PHE A 156 TRP 0.011 0.002 TRP A 153 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 ( 5651) covalent geometry : angle 0.61759 / 0.37 ( 8350) hydrogen bonds : bond 0.07283 / 4.83 ( 216) hydrogen bonds : angle 4.11203 / 3.12 ( 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 26 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.074 Fit side-chains REVERT: A 48 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5577 (tp) REVERT: A 104 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7617 (mtp85) REVERT: A 131 ASN cc_start: 0.7279 (m-40) cc_final: 0.6924 (m-40) REVERT: A 133 TRP cc_start: 0.6665 (p-90) cc_final: 0.5642 (p-90) outliers start: 8 outliers final: 6 residues processed: 25 average time/residue: 0.4685 time to fit residues: 12.2404 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 : 0.094 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.0370 chunk 1 optimal weight: 0.0980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.275672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.247798 restraints weight = 4439.498| |-----------------------------------------------------------------------------| r_work (start): 0.4799 rms_B_bonded: 0.82 r_work (final): 0.4799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5651 Z= 0.134 Angle : 0.588 6.644 8350 Z= 0.354 Chirality : 0.039 0.313 1011 Planarity : 0.005 0.038 519 Dihedral : 25.970 171.152 2435 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.24 % Favored : 91.37 % Rotamer: Outliers : 1.98 % Allowed : 20.30 % 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: -0.32 (0.54), residues: 255 helix: 1.80 (0.48), residues: 119 sheet: -1.68 (0.77), residues: 49 loop : -2.21 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.014 0.002 TYR A 195 PHE 0.015 0.001 PHE A 156 TRP 0.011 0.001 TRP A 153 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 ( 5651) covalent geometry : angle 0.58814 / 0.35 ( 8350) hydrogen bonds : bond 0.06381 / 4.28 ( 216) hydrogen bonds : angle 3.96109 / 3.01 ( 512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1411.80 seconds wall clock time: 24 minutes 50.22 seconds (1490.22 seconds total)