Starting phenix.real_space_refine on Wed Aug 5 13:08:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zif_74272/08_2026/9zif_74272.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zif_74272/08_2026/9zif_74272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zif_74272/08_2026/9zif_74272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zif_74272/08_2026/9zif_74272.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zif_74272/08_2026/9zif_74272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zif_74272/08_2026/9zif_74272.map" } resolution = 3.0 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= 0.007 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 417 5.49 5 Mg 33 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9943 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 26, 'rna2p_pyr': 15, 'rna3p_pur': 217, 'rna3p_pyr': 159} Link IDs: {'rna2p': 41, 'rna3p': 375} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Unusual residues: {' MG': 33} Classifications: {'undetermined': 33, 'water': 1} Link IDs: {None: 33} Time building chain proxies: 2.26, per 1000 atoms: 0.23 Number of scatterers: 9943 At special positions: 0 Unit cell: (120.048, 168.36, 146.4, 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 3 16.00 P 417 15.00 Mg 33 11.99 O 3052 8.00 N 1834 7.00 C 4604 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: 0.80 Conformation dependent library (CDL) restraints added in 74.1 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 44.0% alpha, 17.2% beta 133 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.744A pdb=" N PHE B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 109 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.596A pdb=" N THR B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 80 " --> pdb=" O LEU B 33 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 341 hydrogen bonds 584 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1112 1.33 - 1.45: 5350 1.45 - 1.57: 3700 1.57 - 1.69: 833 1.69 - 1.81: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" C6 G A 357 " pdb=" N1 G A 357 " ideal model delta sigma weight residual 1.391 1.360 0.031 7.00e-03 2.04e+04 1.98e+01 bond pdb=" C4 C A 369 " pdb=" N4 C A 369 " ideal model delta sigma weight residual 1.335 1.297 0.038 9.00e-03 1.23e+04 1.76e+01 bond pdb=" N9 A A 350 " pdb=" C4 A A 350 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.73e+00 bond pdb=" N9 A A 381 " pdb=" C4 A A 381 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.67e+00 bond pdb=" N9 A A 189 " pdb=" C4 A A 189 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.39e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 15515 1.79 - 3.57: 1364 3.57 - 5.36: 53 5.36 - 7.15: 8 7.15 - 8.93: 4 Bond angle restraints: 16944 Sorted by residual: angle pdb=" C5 G A 357 " pdb=" C6 G A 357 " pdb=" O6 G A 357 " ideal model delta sigma weight residual 128.60 136.75 -8.15 6.00e-01 2.78e+00 1.85e+02 angle pdb=" O6 G A 357 " pdb=" C6 G A 357 " pdb=" N1 G A 357 " ideal model delta sigma weight residual 119.90 111.77 8.13 6.00e-01 2.78e+00 1.84e+02 angle pdb=" N3 C A 369 " pdb=" C4 C A 369 " pdb=" N4 C A 369 " ideal model delta sigma weight residual 118.00 109.51 8.49 7.00e-01 2.04e+00 1.47e+02 angle pdb=" N3 C A 369 " pdb=" C4 C A 369 " pdb=" C5 C A 369 " ideal model delta sigma weight residual 121.90 125.18 -3.28 4.00e-01 6.25e+00 6.71e+01 angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 117.86 4.04 7.00e-01 2.04e+00 3.33e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 5960 34.95 - 69.91: 1007 69.91 - 104.86: 141 104.86 - 139.81: 2 139.81 - 174.77: 6 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual 200.00 25.23 174.77 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A 34 " pdb=" C1' U A 34 " pdb=" N1 U A 34 " pdb=" C2 U A 34 " ideal model delta sinusoidal sigma weight residual -160.00 -80.18 -79.82 1 1.50e+01 4.44e-03 3.51e+01 dihedral pdb=" O4' U A 264 " pdb=" C1' U A 264 " pdb=" N1 U A 264 " pdb=" C2 U A 264 " ideal model delta sinusoidal sigma weight residual -128.00 -43.37 -84.63 1 1.70e+01 3.46e-03 3.01e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1578 0.044 - 0.089: 200 0.089 - 0.133: 269 0.133 - 0.178: 171 0.178 - 0.222: 3 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C1' G A 317 " pdb=" O4' G A 317 " pdb=" C2' G A 317 " pdb=" N9 G A 317 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" P G A 372 " pdb=" OP1 G A 372 " pdb=" OP2 G A 372 " pdb=" O5' G A 372 " both_signs ideal model delta sigma weight residual True 2.41 -2.61 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' U A 185 " pdb=" C4' U A 185 " pdb=" O3' U A 185 " pdb=" C2' U A 185 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 369 " 0.011 2.00e-02 2.50e+03 2.73e-02 1.67e+01 pdb=" N1 C A 369 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C A 369 " 0.012 2.00e-02 2.50e+03 pdb=" O2 C A 369 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C A 369 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A 369 " -0.066 2.00e-02 2.50e+03 pdb=" N4 C A 369 " 0.045 2.00e-02 2.50e+03 pdb=" C5 C A 369 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C A 369 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 318 " -0.044 2.00e-02 2.50e+03 2.14e-02 1.03e+01 pdb=" N1 C A 318 " 0.042 2.00e-02 2.50e+03 pdb=" C2 C A 318 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 318 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C A 318 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 318 " -0.008 2.00e-02 2.50e+03 pdb=" N4 C A 318 " -0.012 2.00e-02 2.50e+03 pdb=" C5 C A 318 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A 318 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 317 " 0.041 2.00e-02 2.50e+03 1.76e-02 9.30e+00 pdb=" N9 G A 317 " -0.041 2.00e-02 2.50e+03 pdb=" C8 G A 317 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 317 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 317 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 317 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 317 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G A 317 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 317 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A 317 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G A 317 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G A 317 " -0.004 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 40 2.55 - 3.14: 7023 3.14 - 3.73: 21034 3.73 - 4.31: 27882 4.31 - 4.90: 34402 Nonbonded interactions: 90381 Sorted by model distance: nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 511 " model vdw 1.964 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 511 " model vdw 2.035 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 508 " model vdw 2.073 2.170 nonbonded pdb=" N7 G A 294 " pdb="MG MG A 501 " model vdw 2.115 2.250 nonbonded pdb=" OP2 A A 390 " pdb="MG MG A 504 " model vdw 2.119 2.170 ... (remaining 90376 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: 7.880 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 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 0.048 11000 Z= 0.232 Angle : 0.858 8.931 16944 Z= 0.750 Chirality : 0.063 0.222 2221 Planarity : 0.004 0.027 581 Dihedral : 25.552 174.768 6900 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.04 % Allowed : 36.36 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.90), residues: 114 helix: 1.65 (0.85), residues: 47 sheet: 0.22 (1.17), residues: 23 loop : -1.83 (1.09), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.006 0.001 TYR B 94 PHE 0.003 0.001 PHE B 17 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.23 (11000) covalent geometry : angle 0.85806 / 0.75 (16944) hydrogen bonds : bond 0.09764 / 10.30 ( 390) hydrogen bonds : angle 2.69753 / 3.20 ( 725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.143 Fit side-chains REVERT: B 9 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8637 (mtpp) REVERT: B 11 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 34 ASP cc_start: 0.8900 (m-30) cc_final: 0.8630 (m-30) REVERT: B 35 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7380 (mtt180) outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 0.7676 time to fit residues: 17.0831 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 0.0970 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 overall best weight: 6.4186 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.078547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.044308 restraints weight = 54354.157| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.98 r_work: 0.2677 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 11000 Z= 0.506 Angle : 0.920 13.388 16944 Z= 0.467 Chirality : 0.066 0.317 2221 Planarity : 0.006 0.024 581 Dihedral : 25.781 172.729 6651 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 9.09 % Allowed : 26.26 % Favored : 64.65 % 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: -1.21 (0.76), residues: 114 helix: 0.29 (0.70), residues: 47 sheet: -0.42 (0.93), residues: 26 loop : -2.32 (0.99), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.017 0.003 TYR B 94 PHE 0.015 0.004 PHE B 17 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.51 (11000) covalent geometry : angle 0.91982 / 0.47 (16944) hydrogen bonds : bond 0.11199 / 11.28 ( 390) hydrogen bonds : angle 2.96313 / 3.57 ( 725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.157 Fit side-chains REVERT: B 11 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8625 (mm-30) REVERT: B 26 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7250 (ttp-110) REVERT: B 35 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7647 (mtt180) REVERT: B 70 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8615 (mt-10) REVERT: B 83 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9177 (mm) outliers start: 9 outliers final: 4 residues processed: 24 average time/residue: 0.6965 time to fit residues: 17.6708 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 83 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.078558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044356 restraints weight = 54533.129| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.15 r_work: 0.2684 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11000 Z= 0.327 Angle : 0.702 9.560 16944 Z= 0.379 Chirality : 0.049 0.288 2221 Planarity : 0.005 0.022 581 Dihedral : 25.986 173.393 6647 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 9.09 % Allowed : 28.28 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.79), residues: 114 helix: 1.13 (0.75), residues: 47 sheet: -0.20 (0.87), residues: 26 loop : -2.52 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.012 0.002 TYR B 94 PHE 0.012 0.002 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.33 (11000) covalent geometry : angle 0.70207 / 0.38 (16944) hydrogen bonds : bond 0.09226 / 9.02 ( 390) hydrogen bonds : angle 2.74288 / 3.27 ( 725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.085 Fit side-chains REVERT: B 11 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8541 (mm-30) REVERT: B 35 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7662 (mmt180) outliers start: 9 outliers final: 4 residues processed: 25 average time/residue: 0.7559 time to fit residues: 19.8633 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 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 = 0.3944 r_free = 0.3944 target = 0.077266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.043347 restraints weight = 55083.272| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.77 r_work: 0.2657 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11000 Z= 0.397 Angle : 0.818 13.257 16944 Z= 0.431 Chirality : 0.058 0.307 2221 Planarity : 0.006 0.023 581 Dihedral : 26.162 175.068 6647 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 9.09 % Allowed : 31.31 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.78), residues: 114 helix: 0.98 (0.74), residues: 47 sheet: -0.52 (0.82), residues: 26 loop : -2.61 (1.05), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 26 TYR 0.014 0.003 TYR B 94 PHE 0.019 0.004 PHE B 17 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.40 (11000) covalent geometry : angle 0.81794 / 0.43 (16944) hydrogen bonds : bond 0.11178 / 11.11 ( 390) hydrogen bonds : angle 2.82109 / 3.50 ( 725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.141 Fit side-chains REVERT: B 11 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8593 (mm-30) REVERT: B 12 GLU cc_start: 0.9115 (mp0) cc_final: 0.8506 (mp0) REVERT: B 35 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7906 (mtt180) REVERT: B 91 GLU cc_start: 0.8499 (pm20) cc_final: 0.8223 (pp20) outliers start: 9 outliers final: 4 residues processed: 27 average time/residue: 0.7086 time to fit residues: 20.1347 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 50.0000 chunk 37 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 overall best weight: 6.9790 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.076105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042254 restraints weight = 55064.308| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.95 r_work: 0.2628 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 11000 Z= 0.532 Angle : 0.997 16.011 16944 Z= 0.504 Chirality : 0.069 0.366 2221 Planarity : 0.007 0.042 581 Dihedral : 26.446 178.065 6647 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 11.11 % Allowed : 27.27 % Favored : 61.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.77), residues: 114 helix: 0.49 (0.71), residues: 47 sheet: -0.43 (0.86), residues: 26 loop : -2.59 (1.05), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.023 0.004 TYR B 94 PHE 0.026 0.004 PHE B 17 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.53 (11000) covalent geometry : angle 0.99673 / 0.50 (16944) hydrogen bonds : bond 0.12692 / 12.51 ( 390) hydrogen bonds : angle 3.21452 / 3.98 ( 725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.172 Fit side-chains REVERT: B 11 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8582 (mm-30) REVERT: B 26 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7357 (ttp-110) REVERT: B 35 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8093 (mmt90) REVERT: B 83 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9154 (mm) REVERT: B 91 GLU cc_start: 0.8493 (pm20) cc_final: 0.8194 (pp20) outliers start: 11 outliers final: 6 residues processed: 24 average time/residue: 0.7479 time to fit residues: 19.1162 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 40.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 30.0000 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.077635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.043895 restraints weight = 55519.087| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 0.99 r_work: 0.2697 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11000 Z= 0.196 Angle : 0.616 8.662 16944 Z= 0.354 Chirality : 0.043 0.284 2221 Planarity : 0.005 0.028 581 Dihedral : 26.338 178.872 6647 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 34.34 % Favored : 60.61 % 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: -0.38 (0.82), residues: 114 helix: 1.80 (0.79), residues: 47 sheet: -0.69 (0.77), residues: 26 loop : -2.48 (1.07), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.015 0.002 TYR B 94 PHE 0.006 0.001 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.20 (11000) covalent geometry : angle 0.61646 / 0.35 (16944) hydrogen bonds : bond 0.09287 / 9.02 ( 390) hydrogen bonds : angle 2.73305 / 3.35 ( 725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.101 Fit side-chains REVERT: B 11 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8565 (mp0) REVERT: B 12 GLU cc_start: 0.9101 (mp0) cc_final: 0.8473 (mp0) REVERT: B 19 GLN cc_start: 0.9089 (mt0) cc_final: 0.8773 (mp10) REVERT: B 91 GLU cc_start: 0.8523 (pm20) cc_final: 0.8220 (pp20) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.8186 time to fit residues: 21.6525 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.075316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.041344 restraints weight = 54959.090| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.29 r_work: 0.2600 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 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 : 0.012 0.107 11000 Z= 0.722 Angle : 1.192 18.912 16944 Z= 0.576 Chirality : 0.081 0.359 2221 Planarity : 0.008 0.048 581 Dihedral : 26.410 177.870 6647 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 35.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 5.05 % Allowed : 35.35 % Favored : 59.60 % 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: -1.62 (0.75), residues: 114 helix: 0.03 (0.72), residues: 47 sheet: -0.57 (0.81), residues: 26 loop : -2.70 (1.00), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 106 TYR 0.017 0.004 TYR B 94 PHE 0.025 0.004 PHE B 17 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.72 (11000) covalent geometry : angle 1.19241 / 0.58 (16944) hydrogen bonds : bond 0.14224 / 14.14 ( 390) hydrogen bonds : angle 3.39728 / 4.21 ( 725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.114 Fit side-chains REVERT: B 11 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8682 (mm-30) REVERT: B 91 GLU cc_start: 0.8607 (pm20) cc_final: 0.8263 (pp20) outliers start: 5 outliers final: 4 residues processed: 18 average time/residue: 0.8792 time to fit residues: 16.6198 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 83 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 overall best weight: 7.3788 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.075543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041722 restraints weight = 54489.082| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.78 r_work: 0.2616 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 11000 Z= 0.542 Angle : 1.021 13.896 16944 Z= 0.506 Chirality : 0.070 0.342 2221 Planarity : 0.007 0.038 581 Dihedral : 26.516 178.315 6647 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 29.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 6.06 % Allowed : 33.33 % Favored : 60.61 % 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: -1.22 (0.79), residues: 114 helix: 0.61 (0.78), residues: 47 sheet: -0.50 (0.85), residues: 26 loop : -2.72 (1.02), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 106 TYR 0.012 0.003 TYR B 94 PHE 0.013 0.003 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00885 / 0.54 (11000) covalent geometry : angle 1.02139 / 0.51 (16944) hydrogen bonds : bond 0.12170 / 11.98 ( 390) hydrogen bonds : angle 3.22138 / 4.00 ( 725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.147 Fit side-chains REVERT: B 11 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8653 (mm-30) REVERT: B 91 GLU cc_start: 0.8626 (pm20) cc_final: 0.8327 (pp20) REVERT: B 113 LYS cc_start: 0.8591 (mmtt) cc_final: 0.7988 (tppt) outliers start: 6 outliers final: 4 residues processed: 20 average time/residue: 0.8435 time to fit residues: 17.8167 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 75 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.077028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.045139 restraints weight = 54892.878| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.04 r_work: 0.2692 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11000 Z= 0.223 Angle : 0.617 8.942 16944 Z= 0.356 Chirality : 0.043 0.275 2221 Planarity : 0.005 0.032 581 Dihedral : 26.405 178.653 6647 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 3.03 % Allowed : 37.37 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.79), residues: 114 helix: 1.50 (0.78), residues: 47 sheet: -0.64 (0.76), residues: 26 loop : -2.70 (1.00), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.018 0.002 TYR B 81 PHE 0.013 0.002 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.22 (11000) covalent geometry : angle 0.61727 / 0.36 (16944) hydrogen bonds : bond 0.09396 / 9.32 ( 390) hydrogen bonds : angle 2.73869 / 3.34 ( 725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.143 Fit side-chains REVERT: B 11 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8561 (mp0) REVERT: B 12 GLU cc_start: 0.9109 (mp0) cc_final: 0.8533 (mp0) REVERT: B 19 GLN cc_start: 0.9163 (mt0) cc_final: 0.8855 (mp10) REVERT: B 91 GLU cc_start: 0.8578 (pm20) cc_final: 0.8274 (pp20) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.8373 time to fit residues: 20.2492 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 10.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.075670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.042180 restraints weight = 54281.046| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.56 r_work: 0.2634 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 11000 Z= 0.467 Angle : 0.871 13.664 16944 Z= 0.450 Chirality : 0.062 0.315 2221 Planarity : 0.006 0.035 581 Dihedral : 26.330 178.835 6647 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 3.03 % Allowed : 38.38 % Favored : 58.59 % 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: -1.05 (0.77), residues: 114 helix: 0.99 (0.78), residues: 47 sheet: -0.54 (0.76), residues: 26 loop : -2.87 (0.95), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 106 TYR 0.016 0.003 TYR B 94 PHE 0.015 0.002 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.47 (11000) covalent geometry : angle 0.87146 / 0.45 (16944) hydrogen bonds : bond 0.11385 / 11.42 ( 390) hydrogen bonds : angle 3.02634 / 3.74 ( 725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.145 Fit side-chains REVERT: B 11 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8587 (mm-30) REVERT: B 91 GLU cc_start: 0.8637 (pm20) cc_final: 0.8326 (pp20) REVERT: B 113 LYS cc_start: 0.8516 (mmtt) cc_final: 0.7899 (tppt) outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.8565 time to fit residues: 18.1195 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 50.0000 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.077778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.044400 restraints weight = 55666.684| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.00 r_work: 0.2728 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11000 Z= 0.136 Angle : 0.559 8.421 16944 Z= 0.333 Chirality : 0.038 0.275 2221 Planarity : 0.005 0.034 581 Dihedral : 26.315 178.715 6647 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 3.03 % Allowed : 38.38 % Favored : 58.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.80), residues: 114 helix: 1.81 (0.77), residues: 47 sheet: -0.87 (0.75), residues: 26 loop : -2.47 (1.04), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.020 0.002 TYR B 81 PHE 0.007 0.001 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (11000) covalent geometry : angle 0.55874 / 0.33 (16944) hydrogen bonds : bond 0.08821 / 8.83 ( 390) hydrogen bonds : angle 2.63072 / 3.20 ( 725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4294.59 seconds wall clock time: 73 minutes 48.28 seconds (4428.28 seconds total)