Starting phenix.real_space_refine on Thu Jul 2 05:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo2_26638/07_2026/7uo2_26638.map" } resolution = 3.1 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= 0.012 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: 6 Type Number sf(0) Gaussians P 270 5.49 5 Mg 3 5.21 5 S 2 5.16 5 C 3171 2.51 5 N 1258 2.21 5 O 2031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6735 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 922 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 5810 Classifications: {'RNA': 271} Modifications used: {'5*END': 1, 'rna2p_pur': 29, 'rna2p_pyr': 26, 'rna3p_pur': 122, 'rna3p_pyr': 94} Link IDs: {'rna2p': 55, 'rna3p': 215} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.39, per 1000 atoms: 0.21 Number of scatterers: 6735 At special positions: 0 Unit cell: (88.5636, 124.96, 127.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 2 16.00 P 270 15.00 Mg 3 11.99 O 2031 8.00 N 1258 7.00 C 3171 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: 0.54 Conformation dependent library (CDL) restraints added in 156.7 milliseconds 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 214 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 40.2% alpha, 9.8% beta 81 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.850A pdb=" N LEU A 9 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 10 " --> pdb=" O ARG A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 10' Processing helix chain 'A' and resid 13 through 23 removed outlier: 4.134A pdb=" N PHE A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.956A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.504A pdb=" N LEU A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.850A pdb=" N THR A 33 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 87 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG A 45 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL A 86 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ALA A 88 " --> pdb=" O GLY A 47 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 218 hydrogen bonds 400 hydrogen bond angles 0 basepair planarities 81 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.69 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: 570 1.32 - 1.44: 3614 1.44 - 1.56: 2714 1.56 - 1.69: 539 1.69 - 1.81: 3 Bond restraints: 7440 Sorted by residual: bond pdb=" C2' U B 17 " pdb=" C1' U B 17 " ideal model delta sigma weight residual 1.529 1.508 0.021 1.50e-02 4.44e+03 1.88e+00 bond pdb=" C4' U B 17 " pdb=" C3' U B 17 " ideal model delta sigma weight residual 1.521 1.540 -0.019 1.50e-02 4.44e+03 1.62e+00 bond pdb=" O3' U B 17 " pdb=" P C B 18 " ideal model delta sigma weight residual 1.607 1.624 -0.017 1.50e-02 4.44e+03 1.31e+00 bond pdb=" O4' G B 271 " pdb=" C1' G B 271 " ideal model delta sigma weight residual 1.412 1.429 -0.017 1.50e-02 4.44e+03 1.23e+00 bond pdb=" C4' G B 271 " pdb=" C3' G B 271 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.50e-02 4.44e+03 1.17e+00 ... (remaining 7435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11105 1.49 - 2.98: 235 2.98 - 4.47: 49 4.47 - 5.96: 10 5.96 - 7.44: 1 Bond angle restraints: 11400 Sorted by residual: angle pdb=" C2' G B 271 " pdb=" C1' G B 271 " pdb=" N9 G B 271 " ideal model delta sigma weight residual 112.00 106.53 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C4' U B 17 " pdb=" C3' U B 17 " pdb=" O3' U B 17 " ideal model delta sigma weight residual 113.00 117.92 -4.92 1.50e+00 4.44e-01 1.08e+01 angle pdb=" O4' G B 271 " pdb=" C4' G B 271 " pdb=" C3' G B 271 " ideal model delta sigma weight residual 104.00 100.99 3.01 1.00e+00 1.00e+00 9.05e+00 angle pdb=" C4' G B 271 " pdb=" C3' G B 271 " pdb=" O3' G B 271 " ideal model delta sigma weight residual 113.00 117.45 -4.45 1.50e+00 4.44e-01 8.78e+00 angle pdb=" O4' G B 271 " pdb=" C1' G B 271 " pdb=" N9 G B 271 " ideal model delta sigma weight residual 108.50 112.90 -4.40 1.50e+00 4.44e-01 8.59e+00 ... (remaining 11395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 3527 35.14 - 70.28: 273 70.28 - 105.41: 24 105.41 - 140.55: 4 140.55 - 175.69: 4 Dihedral angle restraints: 3832 sinusoidal: 3507 harmonic: 325 Sorted by residual: dihedral pdb=" O4' U B 257 " pdb=" C1' U B 257 " pdb=" N1 U B 257 " pdb=" C2 U B 257 " ideal model delta sinusoidal sigma weight residual 200.00 51.23 148.77 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U B 331 " pdb=" C1' U B 331 " pdb=" N1 U B 331 " pdb=" C2 U B 331 " ideal model delta sinusoidal sigma weight residual -128.00 47.69 -175.69 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U B 302 " pdb=" C1' U B 302 " pdb=" N1 U B 302 " pdb=" C2 U B 302 " ideal model delta sinusoidal sigma weight residual 232.00 58.14 173.86 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1424 0.058 - 0.116: 58 0.116 - 0.174: 9 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 1493 Sorted by residual: chirality pdb=" C3' G B 271 " pdb=" C4' G B 271 " pdb=" O3' G B 271 " pdb=" C2' G B 271 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1' G B 16 " pdb=" O4' G B 16 " pdb=" C2' G B 16 " pdb=" N9 G B 16 " both_signs ideal model delta sigma weight residual False 2.46 2.66 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1' G B 324 " pdb=" O4' G B 324 " pdb=" C2' G B 324 " pdb=" N9 G B 324 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 1490 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 271 " 0.053 2.00e-02 2.50e+03 2.45e-02 1.81e+01 pdb=" N9 G B 271 " -0.064 2.00e-02 2.50e+03 pdb=" C8 G B 271 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 271 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 271 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 271 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B 271 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G B 271 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 271 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 271 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B 271 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G B 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 17 " 0.015 2.00e-02 2.50e+03 2.20e-02 1.09e+01 pdb=" N1 U B 17 " 0.014 2.00e-02 2.50e+03 pdb=" C2 U B 17 " -0.028 2.00e-02 2.50e+03 pdb=" O2 U B 17 " -0.013 2.00e-02 2.50e+03 pdb=" N3 U B 17 " 0.037 2.00e-02 2.50e+03 pdb=" C4 U B 17 " -0.029 2.00e-02 2.50e+03 pdb=" O4 U B 17 " 0.021 2.00e-02 2.50e+03 pdb=" C5 U B 17 " -0.018 2.00e-02 2.50e+03 pdb=" C6 U B 17 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 16 " -0.042 2.00e-02 2.50e+03 1.73e-02 8.95e+00 pdb=" N9 G B 16 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G B 16 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G B 16 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 16 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 16 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G B 16 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G B 16 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 16 " 0.014 2.00e-02 2.50e+03 pdb=" N2 G B 16 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G B 16 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G B 16 " 0.007 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 175 2.61 - 3.18: 5207 3.18 - 3.75: 13421 3.75 - 4.33: 16769 4.33 - 4.90: 22869 Nonbonded interactions: 58441 Sorted by model distance: nonbonded pdb=" OP1 G B 250 " pdb="MG MG B 403 " model vdw 2.033 2.170 nonbonded pdb=" OP1 A B 67 " pdb="MG MG B 401 " model vdw 2.049 2.170 nonbonded pdb=" OP1 A B 351 " pdb="MG MG B 401 " model vdw 2.066 2.170 nonbonded pdb=" O2' A B 112 " pdb=" OP1 C B 115 " model vdw 2.134 3.040 nonbonded pdb=" O2' G B 262 " pdb=" OP1 U B 263 " model vdw 2.221 3.040 ... (remaining 58436 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.002 0.023 7440 Z= 0.112 Angle : 0.549 7.444 11400 Z= 0.273 Chirality : 0.027 0.290 1493 Planarity : 0.004 0.035 435 Dihedral : 19.036 175.688 3618 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % Rotamer: Outliers : 2.04 % Allowed : 10.20 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.70), residues: 110 helix: -0.20 (0.84), residues: 36 sheet: -1.26 (1.44), residues: 14 loop : -3.74 (0.58), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 PHE 0.004 0.001 PHE A 5 TRP 0.001 0.000 TRP A 108 HIS 0.002 0.000 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.11 ( 7440) covalent geometry : angle 0.54910 / 0.27 (11400) hydrogen bonds : bond 0.06091 / 3.27 ( 242) hydrogen bonds : angle 2.22844 / 1.60 ( 472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.097 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 0.1079 time to fit residues: 4.1283 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.059814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.046289 restraints weight = 55067.821| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.06 r_work: 0.3339 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.110 7440 Z= 0.529 Angle : 1.138 9.475 11400 Z= 0.551 Chirality : 0.056 0.317 1493 Planarity : 0.009 0.060 435 Dihedral : 21.132 172.239 3373 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 27.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 6.12 % Allowed : 13.27 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.65), residues: 110 helix: -1.70 (0.68), residues: 40 sheet: -2.22 (1.05), residues: 14 loop : -3.50 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 10 PHE 0.020 0.004 PHE A 19 TRP 0.005 0.003 TRP A 108 HIS 0.007 0.003 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.01007 / 0.53 ( 7440) covalent geometry : angle 1.13829 / 0.55 (11400) hydrogen bonds : bond 0.12668 / 8.55 ( 242) hydrogen bonds : angle 2.84932 / 1.93 ( 472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8142 (tp-100) outliers start: 6 outliers final: 3 residues processed: 23 average time/residue: 0.0939 time to fit residues: 2.8843 Evaluate side-chains 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.062539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.049128 restraints weight = 54015.971| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.20 r_work: 0.3439 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7440 Z= 0.177 Angle : 0.704 6.816 11400 Z= 0.354 Chirality : 0.037 0.263 1493 Planarity : 0.005 0.035 435 Dihedral : 20.332 174.944 3373 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 1.02 % Allowed : 18.37 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.74), residues: 110 helix: -0.42 (0.85), residues: 40 sheet: -1.75 (1.14), residues: 14 loop : -3.21 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 PHE 0.056 0.004 PHE A 19 TRP 0.004 0.001 TRP A 108 HIS 0.004 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 ( 7440) covalent geometry : angle 0.70398 / 0.35 (11400) hydrogen bonds : bond 0.07114 / 4.71 ( 242) hydrogen bonds : angle 2.24812 / 1.42 ( 472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.104 Fit side-chains REVERT: A 31 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7830 (tp-100) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.1429 time to fit residues: 4.0337 Evaluate side-chains 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.061664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.048109 restraints weight = 56431.836| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.27 r_work: 0.3400 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7440 Z= 0.242 Angle : 0.768 6.811 11400 Z= 0.385 Chirality : 0.040 0.262 1493 Planarity : 0.006 0.036 435 Dihedral : 20.425 173.905 3373 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 7.14 % Allowed : 18.37 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.72), residues: 110 helix: -1.30 (0.75), residues: 45 sheet: -1.51 (1.17), residues: 14 loop : -3.42 (0.76), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 57 PHE 0.006 0.002 PHE A 17 TRP 0.002 0.001 TRP A 108 HIS 0.004 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.24 ( 7440) covalent geometry : angle 0.76771 / 0.38 (11400) hydrogen bonds : bond 0.07560 / 4.97 ( 242) hydrogen bonds : angle 2.34706 / 1.48 ( 472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7094 (mtt180) REVERT: A 31 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7766 (tp-100) outliers start: 7 outliers final: 1 residues processed: 26 average time/residue: 0.1381 time to fit residues: 4.3827 Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 15 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.060994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.047397 restraints weight = 56435.475| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.25 r_work: 0.3378 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7440 Z= 0.292 Angle : 0.824 6.946 11400 Z= 0.411 Chirality : 0.043 0.263 1493 Planarity : 0.006 0.038 435 Dihedral : 20.734 172.616 3373 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 5.10 % Allowed : 21.43 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.74), residues: 110 helix: -1.46 (0.74), residues: 46 sheet: -1.24 (1.13), residues: 14 loop : -3.35 (0.83), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 57 PHE 0.009 0.002 PHE A 17 TRP 0.004 0.002 TRP A 108 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.29 ( 7440) covalent geometry : angle 0.82366 / 0.41 (11400) hydrogen bonds : bond 0.08478 / 5.64 ( 242) hydrogen bonds : angle 2.47524 / 1.56 ( 472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.099 Fit side-chains REVERT: A 31 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7792 (tp-100) outliers start: 5 outliers final: 1 residues processed: 23 average time/residue: 0.0964 time to fit residues: 2.9138 Evaluate side-chains 18 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.061340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.047764 restraints weight = 56236.062| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.28 r_work: 0.3392 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7440 Z= 0.259 Angle : 0.777 6.692 11400 Z= 0.389 Chirality : 0.041 0.258 1493 Planarity : 0.006 0.037 435 Dihedral : 20.592 173.643 3373 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 4.08 % Allowed : 23.47 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.74), residues: 110 helix: -1.46 (0.74), residues: 46 sheet: -1.14 (1.13), residues: 14 loop : -3.31 (0.81), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 PHE 0.009 0.002 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.004 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.26 ( 7440) covalent geometry : angle 0.77653 / 0.39 (11400) hydrogen bonds : bond 0.07838 / 5.18 ( 242) hydrogen bonds : angle 2.40330 / 1.50 ( 472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.100 Fit side-chains REVERT: A 31 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7726 (tp-100) outliers start: 4 outliers final: 1 residues processed: 21 average time/residue: 0.0781 time to fit residues: 2.2837 Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.059156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.045774 restraints weight = 56805.862| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.00 r_work: 0.3324 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.108 7440 Z= 0.513 Angle : 1.111 9.086 11400 Z= 0.538 Chirality : 0.055 0.293 1493 Planarity : 0.008 0.048 435 Dihedral : 21.595 171.678 3373 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 31.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.36 % Favored : 83.64 % Rotamer: Outliers : 3.06 % Allowed : 25.51 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.76), residues: 110 helix: -1.42 (0.81), residues: 40 sheet: -1.54 (1.14), residues: 14 loop : -3.17 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 PHE 0.014 0.003 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.008 0.003 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00971 / 0.51 ( 7440) covalent geometry : angle 1.11134 / 0.54 (11400) hydrogen bonds : bond 0.12174 / 8.13 ( 242) hydrogen bonds : angle 2.88542 / 1.85 ( 472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.097 Fit side-chains REVERT: A 31 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7872 (tp40) REVERT: A 108 TRP cc_start: 0.7865 (m-10) cc_final: 0.7350 (m-10) REVERT: A 109 ARG cc_start: 0.8494 (mtm110) cc_final: 0.7920 (mmt-90) outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 0.1048 time to fit residues: 2.8517 Evaluate side-chains 19 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.062078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.048653 restraints weight = 56280.076| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.19 r_work: 0.3434 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7440 Z= 0.182 Angle : 0.717 6.467 11400 Z= 0.360 Chirality : 0.037 0.263 1493 Planarity : 0.005 0.036 435 Dihedral : 20.529 174.674 3373 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.04 % Allowed : 25.51 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.77), residues: 110 helix: -0.76 (0.83), residues: 40 sheet: -1.19 (1.14), residues: 14 loop : -2.85 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 PHE 0.009 0.002 PHE A 19 TRP 0.008 0.002 TRP A 108 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 ( 7440) covalent geometry : angle 0.71708 / 0.36 (11400) hydrogen bonds : bond 0.06955 / 4.58 ( 242) hydrogen bonds : angle 2.34214 / 1.44 ( 472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.108 Fit side-chains REVERT: A 31 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7705 (tp-100) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0996 time to fit residues: 2.9946 Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.061060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.047540 restraints weight = 56655.156| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.23 r_work: 0.3388 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7440 Z= 0.256 Angle : 0.788 6.814 11400 Z= 0.394 Chirality : 0.041 0.260 1493 Planarity : 0.006 0.037 435 Dihedral : 20.694 173.662 3373 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 4.08 % Allowed : 23.47 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.78), residues: 110 helix: -0.98 (0.83), residues: 40 sheet: -1.12 (1.20), residues: 14 loop : -2.75 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 PHE 0.011 0.002 PHE A 19 TRP 0.006 0.002 TRP A 108 HIS 0.004 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.26 ( 7440) covalent geometry : angle 0.78767 / 0.39 (11400) hydrogen bonds : bond 0.07843 / 5.15 ( 242) hydrogen bonds : angle 2.46281 / 1.52 ( 472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.103 Fit side-chains REVERT: A 31 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7843 (tp-100) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.0791 time to fit residues: 2.4623 Evaluate side-chains 21 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.061878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.048553 restraints weight = 55352.298| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.17 r_work: 0.3424 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7440 Z= 0.202 Angle : 0.718 6.875 11400 Z= 0.362 Chirality : 0.037 0.262 1493 Planarity : 0.005 0.036 435 Dihedral : 20.365 174.548 3373 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 2.04 % Allowed : 25.51 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.79), residues: 110 helix: -0.73 (0.85), residues: 40 sheet: -0.90 (1.23), residues: 14 loop : -2.68 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 PHE 0.010 0.002 PHE A 19 TRP 0.006 0.002 TRP A 108 HIS 0.003 0.002 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.20 ( 7440) covalent geometry : angle 0.71797 / 0.36 (11400) hydrogen bonds : bond 0.06918 / 4.53 ( 242) hydrogen bonds : angle 2.34983 / 1.43 ( 472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 220 Ramachandran restraints generated. 110 Oldfield, 0 Emsley, 110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.093 Fit side-chains REVERT: A 31 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7823 (tp-100) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.0904 time to fit residues: 2.6108 Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.060065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.046672 restraints weight = 56432.201| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.44 r_work: 0.3357 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 7440 Z= 0.363 Angle : 0.911 7.304 11400 Z= 0.451 Chirality : 0.047 0.263 1493 Planarity : 0.007 0.038 435 Dihedral : 20.924 172.739 3373 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 4.08 % Allowed : 24.49 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.80), residues: 110 helix: -1.17 (0.83), residues: 40 sheet: -1.01 (1.19), residues: 14 loop : -2.88 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 56 PHE 0.012 0.002 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.006 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.36 ( 7440) covalent geometry : angle 0.91053 / 0.45 (11400) hydrogen bonds : bond 0.09559 / 6.32 ( 242) hydrogen bonds : angle 2.62122 / 1.65 ( 472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.39 seconds wall clock time: 42 minutes 49.83 seconds (2569.83 seconds total)