Starting phenix.real_space_refine on Wed Aug 5 13:25:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ziw_74286/08_2026/9ziw_74286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ziw_74286/08_2026/9ziw_74286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ziw_74286/08_2026/9ziw_74286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ziw_74286/08_2026/9ziw_74286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ziw_74286/08_2026/9ziw_74286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ziw_74286/08_2026/9ziw_74286.map" } resolution = 3.4 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= 0.006 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 41 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1835 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9951 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': 27, 'rna2p_pyr': 21, 'rna3p_pur': 216, 'rna3p_pyr': 153} Link IDs: {'rna2p': 48, 'rna3p': 368} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Unusual residues: {' MG': 41} Classifications: {'undetermined': 41, 'water': 1} Link IDs: {None: 41} Time building chain proxies: 2.38, per 1000 atoms: 0.24 Number of scatterers: 9951 At special positions: 0 Unit cell: (120.78, 169.824, 142.74, 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 41 11.99 O 3051 8.00 N 1835 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 44.6 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, 15.5% beta 141 base pairs and 218 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.626A pdb=" N LEU B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.934A pdb=" N ALA B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.848A pdb=" N ARG B 42 " --> pdb=" O LYS B 79 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 218 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.08 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: 1263 1.33 - 1.45: 5379 1.45 - 1.57: 3520 1.57 - 1.69: 833 1.69 - 1.81: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.25e+00 bond pdb=" N7 A A 332 " pdb=" C5 A A 332 " ideal model delta sigma weight residual 1.388 1.376 0.012 6.00e-03 2.78e+04 3.99e+00 bond pdb=" N9 G A 203 " pdb=" C4 G A 203 " ideal model delta sigma weight residual 1.375 1.360 0.015 8.00e-03 1.56e+04 3.68e+00 bond pdb=" N9 A A 261 " pdb=" C4 A A 261 " ideal model delta sigma weight residual 1.374 1.363 0.011 6.00e-03 2.78e+04 3.45e+00 bond pdb=" N9 G A 224 " pdb=" C4 G A 224 " ideal model delta sigma weight residual 1.375 1.390 -0.015 8.00e-03 1.56e+04 3.30e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 16163 2.30 - 4.59: 763 4.59 - 6.89: 16 6.89 - 9.18: 1 9.18 - 11.48: 1 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O6 G A 198 " pdb=" C6 G A 198 " pdb=" N1 G A 198 " ideal model delta sigma weight residual 119.90 116.11 3.79 6.00e-01 2.78e+00 3.98e+01 angle pdb=" N3 C A 196 " pdb=" C4 C A 196 " pdb=" N4 C A 196 " ideal model delta sigma weight residual 118.00 113.71 4.29 7.00e-01 2.04e+00 3.76e+01 angle pdb=" O2 C A 202 " pdb=" C2 C A 202 " pdb=" N3 C A 202 " ideal model delta sigma weight residual 121.90 117.69 4.21 7.00e-01 2.04e+00 3.61e+01 angle pdb=" C5 G A 198 " pdb=" C6 G A 198 " pdb=" O6 G A 198 " ideal model delta sigma weight residual 128.60 132.17 -3.57 6.00e-01 2.78e+00 3.54e+01 angle pdb=" O2 C A 153 " pdb=" C2 C A 153 " pdb=" N3 C A 153 " ideal model delta sigma weight residual 121.90 117.75 4.15 7.00e-01 2.04e+00 3.52e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 5917 33.80 - 67.60: 1037 67.60 - 101.40: 148 101.40 - 135.20: 9 135.20 - 169.00: 5 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 -160.00 8.65 -168.65 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 -92.79 -67.21 1 1.50e+01 4.44e-03 2.61e+01 dihedral pdb=" O4' C A 220 " pdb=" C1' C A 220 " pdb=" N1 C A 220 " pdb=" C2 C A 220 " ideal model delta sinusoidal sigma weight residual -128.00 -60.20 -67.80 1 1.70e+01 3.46e-03 2.07e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1573 0.045 - 0.090: 212 0.090 - 0.134: 315 0.134 - 0.179: 117 0.179 - 0.224: 4 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C3' A A 147 " pdb=" C4' A A 147 " pdb=" O3' A A 147 " pdb=" C2' A A 147 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' A A 50 " pdb=" O4' A A 50 " pdb=" C2' A A 50 " pdb=" N9 A A 50 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.91e-01 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 -2.28 -0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 332 " -0.041 2.00e-02 2.50e+03 1.81e-02 9.06e+00 pdb=" N9 A A 332 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A A 332 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 332 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A A 332 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 332 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A A 332 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A A 332 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A A 332 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A A 332 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A A 332 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 198 " -0.020 2.00e-02 2.50e+03 1.55e-02 7.23e+00 pdb=" N9 G A 198 " 0.009 2.00e-02 2.50e+03 pdb=" C8 G A 198 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G A 198 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 198 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 198 " 0.021 2.00e-02 2.50e+03 pdb=" O6 G A 198 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G A 198 " -0.031 2.00e-02 2.50e+03 pdb=" C2 G A 198 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G A 198 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 198 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 198 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 72 " -0.033 2.00e-02 2.50e+03 1.59e-02 6.99e+00 pdb=" N9 A A 72 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A A 72 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A A 72 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 72 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 72 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A A 72 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A A 72 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 72 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 72 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A A 72 " 0.002 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 47 2.51 - 3.11: 6926 3.11 - 3.71: 21351 3.71 - 4.30: 27846 4.30 - 4.90: 35414 Nonbonded interactions: 91584 Sorted by model distance: nonbonded pdb=" OP2 A A 50 " pdb="MG MG A 539 " model vdw 1.913 2.170 nonbonded pdb=" N3 G A 22 " pdb="MG MG A 532 " model vdw 1.926 2.250 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 511 " model vdw 1.929 2.170 nonbonded pdb=" O3' A A 49 " pdb="MG MG A 539 " model vdw 1.942 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 511 " model vdw 1.960 2.170 ... (remaining 91579 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: 10.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 0.039 11000 Z= 0.328 Angle : 0.851 11.476 16944 Z= 0.725 Chirality : 0.063 0.224 2221 Planarity : 0.004 0.024 581 Dihedral : 25.813 169.000 6900 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.08 % Allowed : 33.33 % 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: 0.10 (0.82), residues: 114 helix: 2.20 (0.84), residues: 44 sheet: 0.38 (0.94), residues: 19 loop : -2.13 (0.89), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.005 0.001 TYR B 40 PHE 0.004 0.001 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.33 (11000) covalent geometry : angle 0.85121 / 0.73 (16944) hydrogen bonds : bond 0.07260 / 8.31 ( 406) hydrogen bonds : angle 2.56686 / 3.31 ( 741) *********************** 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 11 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 3 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5936 (mtt180) REVERT: B 68 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7911 (t80) outliers start: 8 outliers final: 6 residues processed: 11 average time/residue: 0.1488 time to fit residues: 2.2713 Evaluate side-chains 11 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 3 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.9990 chunk 48 optimal weight: 0.2980 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 overall best weight: 7.8588 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.080498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043835 restraints weight = 59336.022| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.40 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 11000 Z= 0.500 Angle : 1.072 14.480 16944 Z= 0.513 Chirality : 0.075 0.478 2221 Planarity : 0.006 0.049 581 Dihedral : 26.018 166.383 6663 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 33.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 9.09 % Allowed : 39.39 % Favored : 51.52 % 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: -1.47 (0.76), residues: 114 helix: 0.49 (0.78), residues: 47 sheet: -1.18 (0.83), residues: 24 loop : -2.49 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 65 TYR 0.009 0.002 TYR B 94 PHE 0.009 0.002 PHE B 68 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.50 (11000) covalent geometry : angle 1.07199 / 0.51 (16944) hydrogen bonds : bond 0.13957 / 16.03 ( 406) hydrogen bonds : angle 2.87258 / 3.65 ( 741) *********************** 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 14 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 5 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.4962 (OUTLIER) cc_final: 0.4579 (mt0) outliers start: 9 outliers final: 6 residues processed: 14 average time/residue: 0.1095 time to fit residues: 2.1573 Evaluate side-chains 11 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 4 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 30 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.080418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.043347 restraints weight = 59735.599| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.83 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11000 Z= 0.533 Angle : 1.118 13.000 16944 Z= 0.546 Chirality : 0.075 0.441 2221 Planarity : 0.007 0.050 581 Dihedral : 26.592 167.098 6655 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 41.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 13.13 % Allowed : 37.37 % Favored : 49.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.73), residues: 114 helix: -0.51 (0.71), residues: 47 sheet: -1.90 (0.84), residues: 24 loop : -2.69 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 65 TYR 0.006 0.002 TYR B 40 PHE 0.012 0.003 PHE B 17 HIS 0.009 0.006 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.53 (11000) covalent geometry : angle 1.11762 / 0.55 (16944) hydrogen bonds : bond 0.16067 / 18.46 ( 406) hydrogen bonds : angle 3.01043 / 3.93 ( 741) *********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 4 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.4692 (OUTLIER) cc_final: 0.4337 (mt0) REVERT: B 59 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6196 (mtt180) outliers start: 13 outliers final: 9 residues processed: 17 average time/residue: 0.1516 time to fit residues: 3.4913 Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 4 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 20 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.080663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043760 restraints weight = 59874.468| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.16 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11000 Z= 0.381 Angle : 0.885 9.697 16944 Z= 0.452 Chirality : 0.062 0.374 2221 Planarity : 0.006 0.039 581 Dihedral : 26.524 169.704 6655 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 34.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 17.17 % Allowed : 33.33 % Favored : 49.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.76), residues: 114 helix: -0.05 (0.77), residues: 47 sheet: -1.67 (0.88), residues: 24 loop : -2.62 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 65 TYR 0.006 0.001 TYR B 94 PHE 0.011 0.002 PHE B 17 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.38 (11000) covalent geometry : angle 0.88515 / 0.45 (16944) hydrogen bonds : bond 0.13088 / 14.87 ( 406) hydrogen bonds : angle 2.81523 / 3.72 ( 741) *********************** 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 4 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.4408 (OUTLIER) cc_final: 0.4146 (mt0) REVERT: B 59 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.6068 (mtt180) outliers start: 17 outliers final: 10 residues processed: 21 average time/residue: 0.1392 time to fit residues: 3.9243 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 4 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.080518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.043668 restraints weight = 60262.875| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.90 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 11000 Z= 0.481 Angle : 1.068 11.895 16944 Z= 0.524 Chirality : 0.073 0.414 2221 Planarity : 0.007 0.039 581 Dihedral : 26.624 167.457 6655 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 42.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 16.16 % Allowed : 33.33 % Favored : 50.51 % 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: -2.55 (0.75), residues: 114 helix: -0.26 (0.73), residues: 47 sheet: -2.35 (0.84), residues: 24 loop : -2.85 (0.97), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.015 0.002 TYR B 40 PHE 0.012 0.002 PHE B 17 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.48 (11000) covalent geometry : angle 1.06825 / 0.52 (16944) hydrogen bonds : bond 0.15481 / 17.62 ( 406) hydrogen bonds : angle 3.03041 / 3.99 ( 741) *********************** 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 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 4 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 TYR cc_start: 0.4828 (OUTLIER) cc_final: 0.4466 (m-80) REVERT: B 27 GLN cc_start: 0.4319 (OUTLIER) cc_final: 0.3927 (mt0) REVERT: B 59 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.6056 (mtt180) REVERT: B 91 GLU cc_start: 0.1641 (OUTLIER) cc_final: 0.1019 (tt0) outliers start: 16 outliers final: 10 residues processed: 20 average time/residue: 0.1398 time to fit residues: 3.7801 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 4 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 21 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 50.0000 chunk 42 optimal weight: 9.9990 overall best weight: 9.5990 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.080377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046477 restraints weight = 61192.430| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.30 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 11000 Z= 0.593 Angle : 1.281 14.728 16944 Z= 0.611 Chirality : 0.085 0.439 2221 Planarity : 0.008 0.047 581 Dihedral : 26.877 166.742 6655 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 51.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 12.12 % Allowed : 38.38 % Favored : 49.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.76), residues: 114 helix: -0.94 (0.74), residues: 47 sheet: -3.23 (0.83), residues: 26 loop : -2.84 (0.99), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.015 0.003 TYR B 63 PHE 0.017 0.003 PHE B 17 HIS 0.009 0.006 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.59 (11000) covalent geometry : angle 1.28117 / 0.61 (16944) hydrogen bonds : bond 0.17977 / 20.47 ( 406) hydrogen bonds : angle 3.60604 / 4.84 ( 741) *********************** 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 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 4 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.4274 (m-80) REVERT: B 59 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6328 (mtt180) outliers start: 12 outliers final: 8 residues processed: 16 average time/residue: 0.1476 time to fit residues: 3.1396 Evaluate side-chains 14 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 4 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.080500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.046503 restraints weight = 60153.582| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.52 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11000 Z= 0.473 Angle : 1.048 11.399 16944 Z= 0.522 Chirality : 0.072 0.376 2221 Planarity : 0.007 0.038 581 Dihedral : 26.747 168.427 6653 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 43.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 14.14 % Allowed : 36.36 % Favored : 49.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -3.06 (0.78), residues: 114 helix: -0.53 (0.78), residues: 47 sheet: -3.14 (0.85), residues: 26 loop : -2.89 (0.98), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.006 0.001 TYR B 94 PHE 0.015 0.002 PHE B 17 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.47 (11000) covalent geometry : angle 1.04834 / 0.52 (16944) hydrogen bonds : bond 0.15406 / 17.32 ( 406) hydrogen bonds : angle 3.29570 / 4.45 ( 741) *********************** 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: 14 poor density : 5 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 GLN cc_start: 0.4525 (OUTLIER) cc_final: 0.4131 (pp30) REVERT: B 27 GLN cc_start: 0.4585 (OUTLIER) cc_final: 0.4092 (mt0) REVERT: B 43 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7791 (tp) REVERT: B 59 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6153 (mtt180) REVERT: B 91 GLU cc_start: 0.1477 (OUTLIER) cc_final: 0.0785 (tm-30) outliers start: 14 outliers final: 7 residues processed: 19 average time/residue: 0.1425 time to fit residues: 3.6342 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 5 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 50.0000 chunk 16 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 0.0050 chunk 17 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 5.1800 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.080853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.044608 restraints weight = 60249.547| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.78 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11000 Z= 0.318 Angle : 0.809 8.372 16944 Z= 0.432 Chirality : 0.058 0.326 2221 Planarity : 0.006 0.045 581 Dihedral : 26.593 169.777 6653 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 33.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 13.13 % Allowed : 36.36 % Favored : 50.51 % 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: -2.64 (0.80), residues: 114 helix: -0.07 (0.80), residues: 47 sheet: -3.09 (0.85), residues: 26 loop : -2.70 (0.99), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.008 0.001 TYR B 5 PHE 0.011 0.002 PHE B 17 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.32 (11000) covalent geometry : angle 0.80939 / 0.43 (16944) hydrogen bonds : bond 0.12729 / 14.29 ( 406) hydrogen bonds : angle 3.06129 / 4.13 ( 741) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 PHE cc_start: 0.4581 (OUTLIER) cc_final: 0.4149 (t80) REVERT: B 19 GLN cc_start: 0.4433 (OUTLIER) cc_final: 0.4144 (pp30) REVERT: B 27 GLN cc_start: 0.4123 (OUTLIER) cc_final: 0.3729 (mt0) REVERT: B 43 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7794 (tt) outliers start: 13 outliers final: 7 residues processed: 18 average time/residue: 0.1527 time to fit residues: 3.6239 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 5 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 6.0386 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.080515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.044513 restraints weight = 59653.509| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.12 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11000 Z= 0.373 Angle : 0.882 9.894 16944 Z= 0.455 Chirality : 0.061 0.339 2221 Planarity : 0.006 0.037 581 Dihedral : 26.554 169.313 6653 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 36.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 12.12 % Allowed : 36.36 % Favored : 51.52 % 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: -2.50 (0.79), residues: 114 helix: -0.07 (0.78), residues: 47 sheet: -2.58 (0.90), residues: 24 loop : -2.83 (0.97), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.010 0.001 TYR B 5 PHE 0.012 0.002 PHE B 17 HIS 0.005 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.37 (11000) covalent geometry : angle 0.88236 / 0.45 (16944) hydrogen bonds : bond 0.13431 / 15.13 ( 406) hydrogen bonds : angle 3.05651 / 4.08 ( 741) *********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 5 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 PHE cc_start: 0.4607 (OUTLIER) cc_final: 0.4212 (t80) REVERT: B 19 GLN cc_start: 0.4430 (OUTLIER) cc_final: 0.4138 (pp30) REVERT: B 27 GLN cc_start: 0.4224 (OUTLIER) cc_final: 0.3823 (mt0) REVERT: B 43 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7611 (tp) outliers start: 12 outliers final: 7 residues processed: 17 average time/residue: 0.1198 time to fit residues: 2.9072 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 5 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.080198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.043631 restraints weight = 60040.655| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 4.03 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 11000 Z= 0.510 Angle : 1.070 11.356 16944 Z= 0.530 Chirality : 0.073 0.399 2221 Planarity : 0.007 0.047 581 Dihedral : 26.672 167.039 6653 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 45.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 12.12 % Allowed : 36.36 % Favored : 51.52 % 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: -2.87 (0.78), residues: 114 helix: -0.41 (0.77), residues: 47 sheet: -2.91 (0.88), residues: 26 loop : -2.84 (0.99), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.009 0.002 TYR B 94 PHE 0.013 0.002 PHE B 17 HIS 0.007 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.51 (11000) covalent geometry : angle 1.07021 / 0.53 (16944) hydrogen bonds : bond 0.15934 / 18.15 ( 406) hydrogen bonds : angle 3.27038 / 4.36 ( 741) ********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 5 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 PHE cc_start: 0.4615 (OUTLIER) cc_final: 0.4222 (t80) REVERT: B 19 GLN cc_start: 0.4502 (OUTLIER) cc_final: 0.4205 (pp30) REVERT: B 27 GLN cc_start: 0.4185 (OUTLIER) cc_final: 0.3771 (mt0) REVERT: B 43 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7515 (tp) outliers start: 12 outliers final: 7 residues processed: 17 average time/residue: 0.1194 time to fit residues: 2.8153 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 5 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 106 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.080230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.043899 restraints weight = 59814.311| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.37 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 11000 Z= 0.423 Angle : 0.974 10.861 16944 Z= 0.490 Chirality : 0.068 0.356 2221 Planarity : 0.006 0.036 581 Dihedral : 26.618 168.841 6653 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 40.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 11.11 % Allowed : 37.37 % Favored : 51.52 % 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: -2.63 (0.80), residues: 114 helix: -0.61 (0.75), residues: 53 sheet: -2.56 (0.92), residues: 24 loop : -2.61 (1.09), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.008 0.001 TYR B 94 PHE 0.012 0.002 PHE B 17 HIS 0.007 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.42 (11000) covalent geometry : angle 0.97353 / 0.49 (16944) hydrogen bonds : bond 0.14247 / 16.12 ( 406) hydrogen bonds : angle 3.14455 / 4.19 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.33 seconds wall clock time: 50 minutes 7.00 seconds (3007.00 seconds total)