Starting phenix.real_space_refine on Fri Sep 11 02:24:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uo2_26638/09_2026/7uo2_26638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo2_26638/09_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_26638/09_2026/7uo2_26638.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uo2_26638/09_2026/7uo2_26638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uo2_26638/09_2026/7uo2_26638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo2_26638/09_2026/7uo2_26638.map" model { file = "/net/cci-nas-00/data/ceres_data/7uo2_26638/09_2026/7uo2_26638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo2_26638/09_2026/7uo2_26638.cif" } 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-2.2.1-6174/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: {'RNAv2': 271} Modifications used: {'rna2p_pur': 29, 'rna2p_pyr': 26, 'rna3p_pur': 122, 'rna3p_pyr': 94} Link IDs: {'rna2p': 55, 'rna3p': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 1.66, per 1000 atoms: 0.25 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 261.3 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: 1.17 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: 1.45 Time building geometry restraints manager: 0.76 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=" O3' U B 17 " pdb=" P C B 18 " ideal model delta sigma weight residual 1.607 1.624 -0.017 1.20e-02 6.94e+03 2.04e+00 bond pdb=" C3' C B 374 " pdb=" O3' C B 374 " ideal model delta sigma weight residual 1.415 1.439 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" O3' G B 16 " pdb=" P U B 17 " ideal model delta sigma weight residual 1.607 1.621 -0.014 1.20e-02 6.94e+03 1.38e+00 bond pdb=" C2 G B 16 " pdb=" N3 G B 16 " ideal model delta sigma weight residual 1.323 1.302 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C2' U B 17 " pdb=" C1' U B 17 " ideal model delta sigma weight residual 1.529 1.508 0.021 2.00e-02 2.50e+03 1.06e+00 ... (remaining 7435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10192 1.49 - 2.98: 904 2.98 - 4.47: 217 4.47 - 5.96: 86 5.96 - 7.44: 1 Bond angle restraints: 11400 Sorted by residual: angle pdb=" C3' C B 374 " pdb=" O3' C B 374 " pdb=" P C B 375 " ideal model delta sigma weight residual 119.70 124.49 -4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" C3' C B 237 " pdb=" O3' C B 237 " pdb=" P C B 238 " ideal model delta sigma weight residual 119.70 124.11 -4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" C3' U B 272 " pdb=" O3' U B 272 " pdb=" P A B 273 " ideal model delta sigma weight residual 119.70 123.27 -3.57 1.20e+00 6.94e-01 8.83e+00 angle pdb=" C2' G B 271 " pdb=" C1' G B 271 " pdb=" N9 G B 271 " ideal model delta sigma weight residual 112.40 106.53 5.87 2.00e+00 2.50e-01 8.61e+00 angle pdb=" C3' G B 82 " pdb=" C2' G B 82 " pdb=" O2' G B 82 " ideal model delta sigma weight residual 109.80 115.50 -5.70 2.00e+00 2.50e-01 8.11e+00 ... (remaining 11395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 2930 24.53 - 49.06: 503 49.06 - 73.58: 383 73.58 - 98.11: 14 98.11 - 122.64: 2 Dihedral angle restraints: 3832 sinusoidal: 3507 harmonic: 325 Sorted by residual: dihedral pdb=" C4' G B 82 " pdb=" C3' G B 82 " pdb=" C2' G B 82 " pdb=" C1' G B 82 " ideal model delta sinusoidal sigma weight residual 36.35 -39.45 75.79 1 3.10e+00 1.04e-01 7.54e+02 dihedral pdb=" C4' G B 262 " pdb=" C3' G B 262 " pdb=" C2' G B 262 " pdb=" C1' G B 262 " ideal model delta sinusoidal sigma weight residual 36.34 -38.60 74.95 1 3.10e+00 1.04e-01 7.40e+02 dihedral pdb=" C4' C B 123 " pdb=" C3' C B 123 " pdb=" C2' C B 123 " pdb=" C1' C B 123 " ideal model delta sinusoidal sigma weight residual 36.34 -38.25 74.60 1 3.10e+00 1.04e-01 7.34e+02 ... (remaining 3829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1068 0.072 - 0.143: 40 0.143 - 0.215: 12 0.215 - 0.287: 354 0.287 - 0.358: 19 Chirality restraints: 1493 Sorted by residual: chirality pdb=" P C B 375 " pdb=" OP1 C B 375 " pdb=" OP2 C B 375 " pdb=" O5' C B 375 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C3' G B 262 " pdb=" C4' G B 262 " pdb=" O3' G B 262 " pdb=" C2' G B 262 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.42e+00 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 -2.50 -2.19 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (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: 5.340 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- 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 : 0.003 0.024 7440 Z= 0.157 Angle : 1.030 7.444 11400 Z= 0.412 Chirality : 0.127 0.358 1493 Planarity : 0.004 0.035 435 Dihedral : 25.252 122.641 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 0.00310 / 0.16 ( 7440) covalent geometry : angle 1.03000 / 0.41 (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 : 0.075 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 0.1060 time to fit residues: 3.9798 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 : 0.071 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.060918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.047757 restraints weight = 56620.031| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.33 r_work: 0.3396 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.081 7440 Z= 0.527 Angle : 1.941 18.342 11400 Z= 0.747 Chirality : 0.145 1.586 1493 Planarity : 0.008 0.048 435 Dihedral : 23.298 179.546 3373 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 30.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 5.10 % Allowed : 14.29 % 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: -3.46 (0.68), residues: 110 helix: -0.96 (0.74), residues: 39 sheet: -1.88 (1.13), residues: 14 loop : -3.52 (0.68), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 10 PHE 0.029 0.004 PHE A 19 TRP 0.004 0.002 TRP A 108 HIS 0.006 0.003 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01061 / 0.53 ( 7440) covalent geometry : angle 1.94122 / 0.75 (11400) hydrogen bonds : bond 0.13248 / 8.63 ( 242) hydrogen bonds : angle 2.96820 / 2.01 ( 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 27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8062 (tp-100) REVERT: A 105 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7749 (mm-30) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.1027 time to fit residues: 3.3191 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 : 0.076 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.063679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.050747 restraints weight = 55041.015| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.12 r_work: 0.3496 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7440 Z= 0.233 Angle : 1.395 15.618 11400 Z= 0.543 Chirality : 0.106 0.823 1493 Planarity : 0.006 0.036 435 Dihedral : 23.451 179.809 3373 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 5.10 % Allowed : 15.31 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.74), residues: 110 helix: -0.33 (0.83), residues: 40 sheet: -1.26 (1.25), residues: 14 loop : -3.14 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 113 PHE 0.048 0.004 PHE A 19 TRP 0.001 0.001 TRP A 108 HIS 0.005 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 ( 7440) covalent geometry : angle 1.39461 / 0.54 (11400) hydrogen bonds : bond 0.07894 / 5.31 ( 242) hydrogen bonds : angle 2.32088 / 1.50 ( 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 27 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7820 (tp-100) outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.1236 time to fit residues: 3.9667 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 : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 86 VAL 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: 3.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.062854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.049778 restraints weight = 56256.739| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.18 r_work: 0.3459 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7440 Z= 0.271 Angle : 1.419 15.594 11400 Z= 0.555 Chirality : 0.108 0.918 1493 Planarity : 0.006 0.037 435 Dihedral : 23.505 177.935 3373 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 7.14 % Allowed : 16.33 % Favored : 76.53 % 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: -3.19 (0.74), residues: 110 helix: -1.01 (0.77), residues: 45 sheet: -1.42 (1.25), residues: 14 loop : -3.44 (0.75), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 113 PHE 0.005 0.002 PHE A 19 TRP 0.003 0.001 TRP A 108 HIS 0.004 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 ( 7440) covalent geometry : angle 1.41883 / 0.55 (11400) hydrogen bonds : bond 0.08069 / 5.36 ( 242) hydrogen bonds : angle 2.44686 / 1.55 ( 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 28 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6973 (mtt180) REVERT: A 31 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7651 (tp-100) outliers start: 7 outliers final: 2 residues processed: 27 average time/residue: 0.1087 time to fit residues: 3.6447 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 : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.061043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.047613 restraints weight = 58441.591| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.54 r_work: 0.3387 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 7440 Z= 0.367 Angle : 1.548 16.409 11400 Z= 0.604 Chirality : 0.116 0.939 1493 Planarity : 0.007 0.039 435 Dihedral : 23.795 178.342 3373 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 7.14 % Allowed : 22.45 % Favored : 70.41 % 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: -3.42 (0.74), residues: 110 helix: -1.32 (0.75), residues: 45 sheet: -1.43 (1.22), residues: 14 loop : -3.47 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 10 PHE 0.056 0.004 PHE A 19 TRP 0.006 0.002 TRP A 108 HIS 0.005 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.37 ( 7440) covalent geometry : angle 1.54833 / 0.60 (11400) hydrogen bonds : bond 0.09591 / 6.33 ( 242) hydrogen bonds : angle 2.62788 / 1.70 ( 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 26 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.112 Fit side-chains REVERT: A 10 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7355 (mtt180) REVERT: A 31 GLN cc_start: 0.8431 (tp-100) cc_final: 0.7899 (tp-100) outliers start: 7 outliers final: 4 residues processed: 25 average time/residue: 0.0960 time to fit residues: 3.1171 Evaluate side-chains 22 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.061749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.048459 restraints weight = 58471.651| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.43 r_work: 0.3418 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7440 Z= 0.298 Angle : 1.434 15.559 11400 Z= 0.560 Chirality : 0.108 0.875 1493 Planarity : 0.006 0.038 435 Dihedral : 23.777 179.945 3373 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 5.10 % Allowed : 22.45 % 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: -3.35 (0.74), residues: 110 helix: -1.38 (0.74), residues: 46 sheet: -1.36 (1.19), residues: 14 loop : -3.34 (0.81), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 61 PHE 0.055 0.004 PHE A 19 TRP 0.004 0.002 TRP A 108 HIS 0.005 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.30 ( 7440) covalent geometry : angle 1.43443 / 0.56 (11400) hydrogen bonds : bond 0.08329 / 5.51 ( 242) hydrogen bonds : angle 2.46187 / 1.57 ( 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 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.137 Fit side-chains REVERT: A 10 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7396 (mtt180) REVERT: A 31 GLN cc_start: 0.8372 (tp-100) cc_final: 0.7804 (tp-100) outliers start: 5 outliers final: 2 residues processed: 23 average time/residue: 0.1235 time to fit residues: 3.5250 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.059845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.046521 restraints weight = 58673.075| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.57 r_work: 0.3351 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 7440 Z= 0.483 Angle : 1.715 16.887 11400 Z= 0.666 Chirality : 0.128 1.110 1493 Planarity : 0.008 0.040 435 Dihedral : 23.951 179.883 3373 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 26.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.36 % Favored : 83.64 % Rotamer: Outliers : 5.10 % Allowed : 22.45 % 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: -3.36 (0.76), residues: 110 helix: -1.28 (0.81), residues: 40 sheet: -1.92 (1.06), residues: 14 loop : -3.12 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 10 PHE 0.056 0.005 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.007 0.003 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00976 / 0.48 ( 7440) covalent geometry : angle 1.71531 / 0.67 (11400) hydrogen bonds : bond 0.11562 / 7.54 ( 242) hydrogen bonds : angle 2.84824 / 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 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.104 Fit side-chains REVERT: A 10 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7349 (mtt180) REVERT: A 31 GLN cc_start: 0.8441 (tp-100) cc_final: 0.7933 (tp40) outliers start: 5 outliers final: 1 residues processed: 22 average time/residue: 0.0814 time to fit residues: 2.3750 Evaluate side-chains 20 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG 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: 4.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.063021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.049962 restraints weight = 58689.797| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.43 r_work: 0.3470 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7440 Z= 0.217 Angle : 1.336 14.717 11400 Z= 0.522 Chirality : 0.101 0.883 1493 Planarity : 0.006 0.036 435 Dihedral : 23.574 179.994 3373 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.06 % Allowed : 24.49 % 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: -2.79 (0.76), residues: 110 helix: -0.70 (0.82), residues: 40 sheet: -1.28 (1.21), residues: 14 loop : -2.98 (0.79), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 56 PHE 0.055 0.004 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 ( 7440) covalent geometry : angle 1.33597 / 0.52 (11400) hydrogen bonds : bond 0.07276 / 4.93 ( 242) hydrogen bonds : angle 2.34713 / 1.49 ( 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: 3 poor density : 20 time to evaluate : 0.090 Fit side-chains REVERT: A 31 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7780 (tp-100) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0949 time to fit residues: 2.7428 Evaluate side-chains 23 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 VAL 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: 3.9990 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.062394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.049152 restraints weight = 58538.509| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.42 r_work: 0.3441 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7440 Z= 0.251 Angle : 1.366 14.635 11400 Z= 0.534 Chirality : 0.104 0.858 1493 Planarity : 0.006 0.037 435 Dihedral : 23.550 179.022 3373 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 16.91 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: -3.16 (0.76), residues: 110 helix: -1.31 (0.75), residues: 46 sheet: -1.20 (1.25), residues: 14 loop : -3.17 (0.83), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 PHE 0.057 0.004 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.004 0.002 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.25 ( 7440) covalent geometry : angle 1.36581 / 0.53 (11400) hydrogen bonds : bond 0.07690 / 5.12 ( 242) hydrogen bonds : angle 2.43987 / 1.53 ( 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 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.057 Fit side-chains REVERT: A 31 GLN cc_start: 0.8411 (tp-100) cc_final: 0.7877 (tp-100) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.1113 time to fit residues: 3.1916 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 : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 VAL 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: 0.9980 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.064914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.052384 restraints weight = 56097.763| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.21 r_work: 0.3564 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7440 Z= 0.177 Angle : 1.253 13.855 11400 Z= 0.491 Chirality : 0.095 0.835 1493 Planarity : 0.005 0.034 435 Dihedral : 23.331 177.883 3373 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.04 % Allowed : 24.49 % 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: -2.69 (0.76), residues: 110 helix: -0.92 (0.77), residues: 46 sheet: -0.88 (1.30), residues: 14 loop : -2.93 (0.81), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 69 PHE 0.067 0.004 PHE A 19 TRP 0.004 0.001 TRP A 108 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 ( 7440) covalent geometry : angle 1.25324 / 0.49 (11400) hydrogen bonds : bond 0.06796 / 4.74 ( 242) hydrogen bonds : angle 2.20685 / 1.35 ( 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 24 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.105 Fit side-chains REVERT: A 22 GLN cc_start: 0.8232 (pp30) cc_final: 0.7947 (pp30) REVERT: A 31 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7703 (tp-100) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0976 time to fit residues: 2.9406 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 : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.061204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.047809 restraints weight = 57686.194| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.52 r_work: 0.3397 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 7440 Z= 0.355 Angle : 1.497 15.114 11400 Z= 0.585 Chirality : 0.113 0.959 1493 Planarity : 0.007 0.038 435 Dihedral : 23.635 179.885 3373 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 5.10 % Allowed : 23.47 % 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: -3.29 (0.76), residues: 110 helix: -1.53 (0.75), residues: 46 sheet: -1.20 (1.24), residues: 14 loop : -3.13 (0.84), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 109 PHE 0.063 0.005 PHE A 19 TRP 0.005 0.002 TRP A 108 HIS 0.005 0.003 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.35 ( 7440) covalent geometry : angle 1.49698 / 0.59 (11400) hydrogen bonds : bond 0.09285 / 6.12 ( 242) hydrogen bonds : angle 2.60774 / 1.65 ( 472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.10 seconds wall clock time: 41 minutes 47.11 seconds (2507.11 seconds total)