Starting phenix.real_space_refine on Wed Aug 5 13:07:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zih_74274/08_2026/9zih_74274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zih_74274/08_2026/9zih_74274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zih_74274/08_2026/9zih_74274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zih_74274/08_2026/9zih_74274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zih_74274/08_2026/9zih_74274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zih_74274/08_2026/9zih_74274.map" } resolution = 3.07 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 38 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 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 3 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: 9947 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': 32, 'rna2p_pyr': 17, 'rna3p_pur': 211, 'rna3p_pyr': 157} Link IDs: {'rna2p': 49, 'rna3p': 367} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Unusual residues: {' MG': 38} Classifications: {'undetermined': 38} Link IDs: {None: 37} Time building chain proxies: 2.30, per 1000 atoms: 0.23 Number of scatterers: 9947 At special positions: 0 Unit cell: (122.244, 179.34, 145.668, 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 38 11.99 O 3051 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: 0.86 Conformation dependent library (CDL) restraints added in 47.2 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: 5 helices and 1 sheets defined 48.3% alpha, 16.4% beta 127 base pairs and 204 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.711A pdb=" N ARG B 6 " --> pdb=" O LYS B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.931A pdb=" N GLU B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 6.082A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 574 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 204 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.23 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: 1204 1.33 - 1.45: 5232 1.45 - 1.57: 3726 1.57 - 1.69: 833 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 216 " pdb=" C4 A A 216 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.82e+00 bond pdb=" N9 A A 350 " pdb=" C4 A A 350 " ideal model delta sigma weight residual 1.374 1.385 -0.011 6.00e-03 2.78e+04 3.55e+00 bond pdb=" N9 A A 48 " pdb=" C4 A A 48 " ideal model delta sigma weight residual 1.374 1.364 0.010 6.00e-03 2.78e+04 2.82e+00 bond pdb=" N3 A A 48 " pdb=" C4 A A 48 " ideal model delta sigma weight residual 1.344 1.334 0.010 6.00e-03 2.78e+04 2.67e+00 bond pdb=" N1 U A 35 " pdb=" C2 U A 35 " ideal model delta sigma weight residual 1.381 1.396 -0.015 9.00e-03 1.23e+04 2.65e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 16928 5.40 - 10.79: 14 10.79 - 16.19: 0 16.19 - 21.58: 0 21.58 - 26.98: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O3' A A 409 " pdb=" P U A 410 " pdb=" OP1 U A 410 " ideal model delta sigma weight residual 108.00 81.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" O3' A A 409 " pdb=" P U A 410 " pdb=" OP2 U A 410 " ideal model delta sigma weight residual 108.00 84.37 23.63 3.00e+00 1.11e-01 6.20e+01 angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 117.84 4.06 7.00e-01 2.04e+00 3.36e+01 angle pdb=" C3' U A 264 " pdb=" O3' U A 264 " pdb=" P G A 265 " ideal model delta sigma weight residual 119.70 126.62 -6.92 1.20e+00 6.94e-01 3.33e+01 angle pdb=" C3' U A 371 " pdb=" O3' U A 371 " pdb=" P G A 372 " ideal model delta sigma weight residual 119.70 125.57 -5.87 1.20e+00 6.94e-01 2.39e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 5962 35.45 - 70.90: 1012 70.90 - 106.34: 134 106.34 - 141.79: 4 141.79 - 177.24: 4 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" C5' C A 378 " pdb=" C4' C A 378 " pdb=" C3' C A 378 " pdb=" O3' C A 378 " ideal model delta sinusoidal sigma weight residual 147.00 78.02 68.98 1 8.00e+00 1.56e-02 9.62e+01 dihedral pdb=" C4' C A 378 " pdb=" C3' C A 378 " pdb=" C2' C A 378 " pdb=" C1' C A 378 " ideal model delta sinusoidal sigma weight residual -35.00 33.76 -68.76 1 8.00e+00 1.56e-02 9.57e+01 dihedral pdb=" O4' C A 378 " pdb=" C4' C A 378 " pdb=" C3' C A 378 " pdb=" C2' C A 378 " ideal model delta sinusoidal sigma weight residual 24.00 -34.95 58.95 1 8.00e+00 1.56e-02 7.26e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.395: 2220 0.395 - 0.791: 0 0.791 - 1.186: 0 1.186 - 1.582: 0 1.582 - 1.977: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P U A 410 " pdb=" OP1 U A 410 " pdb=" OP2 U A 410 " pdb=" O5' U A 410 " both_signs ideal model delta sigma weight residual True 2.41 0.43 1.98 2.00e-01 2.50e+01 9.77e+01 chirality pdb=" C3' C A 378 " pdb=" C4' C A 378 " pdb=" O3' C A 378 " pdb=" C2' C A 378 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1' G A 214 " pdb=" O4' G A 214 " pdb=" C2' G A 214 " pdb=" N9 G A 214 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.033 2.00e-02 2.50e+03 1.39e-02 5.84e+00 pdb=" N9 G A 298 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 214 " -0.029 2.00e-02 2.50e+03 1.26e-02 4.77e+00 pdb=" N9 G A 214 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G A 214 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 214 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 214 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 214 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G A 214 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G A 214 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 214 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G A 214 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A 214 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G A 214 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 46 " 0.029 2.00e-02 2.50e+03 1.24e-02 4.62e+00 pdb=" N9 G A 46 " -0.030 2.00e-02 2.50e+03 pdb=" C8 G A 46 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 46 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 46 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 46 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A 46 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G A 46 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 46 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G A 46 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 46 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 46 " -0.003 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 40 2.53 - 3.12: 6986 3.12 - 3.72: 21021 3.72 - 4.31: 27708 4.31 - 4.90: 35371 Nonbonded interactions: 91126 Sorted by model distance: nonbonded pdb=" OP2 C A 103 " pdb="MG MG A 509 " model vdw 1.941 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 511 " model vdw 1.968 2.170 nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 508 " model vdw 1.973 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 512 " model vdw 1.989 2.170 nonbonded pdb=" O4 U A 393 " pdb="MG MG A 538 " model vdw 1.994 2.170 ... (remaining 91121 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: 11.260 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: 0.470 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.730 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: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 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 0.044 11000 Z= 0.297 Angle : 0.901 26.975 16944 Z= 0.726 Chirality : 0.077 1.977 2221 Planarity : 0.004 0.014 581 Dihedral : 25.637 177.237 6900 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 30.30 % Favored : 69.70 % 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: 1.01 (0.82), residues: 114 helix: 2.36 (0.79), residues: 47 sheet: 0.56 (0.88), residues: 26 loop : -1.32 (1.06), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.007 0.001 TYR B 94 PHE 0.007 0.001 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.30 (11000) covalent geometry : angle 0.90097 / 0.73 (16944) hydrogen bonds : bond 0.10113 / 10.26 ( 375) hydrogen bonds : angle 5.03687 / 6.40 ( 703) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.101 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0665 time to fit residues: 1.9189 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 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 = 0.4001 r_free = 0.4001 target = 0.084557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.047020 restraints weight = 50307.646| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.87 r_work: 0.2681 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 11000 Z= 0.508 Angle : 0.979 26.494 16944 Z= 0.482 Chirality : 0.077 1.864 2221 Planarity : 0.006 0.034 581 Dihedral : 25.783 176.359 6645 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.04 % Allowed : 22.22 % Favored : 73.74 % 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: 0.21 (0.79), residues: 114 helix: 1.21 (0.76), residues: 48 sheet: 0.24 (0.89), residues: 26 loop : -1.20 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG B 35 TYR 0.015 0.003 TYR B 81 PHE 0.022 0.005 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.51 (11000) covalent geometry : angle 0.97854 / 0.48 (16944) hydrogen bonds : bond 0.12408 / 13.62 ( 375) hydrogen bonds : angle 2.80869 / 3.52 ( 703) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.143 Fit side-chains REVERT: B 12 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8857 (mt-10) outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 0.0802 time to fit residues: 2.2042 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 91 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 50.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 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 = 0.4017 r_free = 0.4017 target = 0.084834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048475 restraints weight = 50343.403| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.29 r_work: 0.2703 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11000 Z= 0.373 Angle : 0.800 26.379 16944 Z= 0.409 Chirality : 0.066 1.914 2221 Planarity : 0.005 0.022 581 Dihedral : 25.829 173.128 6645 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.81), residues: 114 helix: 1.66 (0.75), residues: 48 sheet: 0.03 (0.87), residues: 26 loop : -1.03 (1.14), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.007 0.002 TYR B 94 PHE 0.020 0.004 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.37 (11000) covalent geometry : angle 0.79998 / 0.41 (16944) hydrogen bonds : bond 0.09658 / 10.67 ( 375) hydrogen bonds : angle 2.67902 / 3.34 ( 703) *********************** 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 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.142 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 18 average time/residue: 0.1032 time to fit residues: 2.7315 Evaluate side-chains 14 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 50.0000 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 50.0000 chunk 12 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.084840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.048791 restraints weight = 50228.864| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.15 r_work: 0.2705 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11000 Z= 0.318 Angle : 0.764 26.572 16944 Z= 0.392 Chirality : 0.064 1.894 2221 Planarity : 0.006 0.052 581 Dihedral : 25.794 173.904 6645 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.03 % Allowed : 18.18 % Favored : 78.79 % 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: 0.79 (0.84), residues: 114 helix: 1.51 (0.76), residues: 48 sheet: 0.30 (0.86), residues: 26 loop : -0.42 (1.24), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 106 TYR 0.011 0.002 TYR B 94 PHE 0.022 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.32 (11000) covalent geometry : angle 0.76423 / 0.39 (16944) hydrogen bonds : bond 0.09843 / 10.71 ( 375) hydrogen bonds : angle 2.55827 / 3.26 ( 703) *********************** 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 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.090 Fit side-chains REVERT: B 35 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7638 (mtp85) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.0843 time to fit residues: 2.1950 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 91 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 41 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 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 = 0.4024 r_free = 0.4024 target = 0.084928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048941 restraints weight = 50077.493| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.11 r_work: 0.2725 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11000 Z= 0.273 Angle : 0.702 26.365 16944 Z= 0.368 Chirality : 0.061 1.916 2221 Planarity : 0.005 0.026 581 Dihedral : 25.771 174.565 6645 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 23.23 % Favored : 76.77 % 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: 1.09 (0.85), residues: 114 helix: 1.78 (0.74), residues: 48 sheet: 0.47 (0.91), residues: 26 loop : -0.32 (1.27), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.010 0.002 TYR B 94 PHE 0.017 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.27 (11000) covalent geometry : angle 0.70176 / 0.37 (16944) hydrogen bonds : bond 0.08964 / 9.70 ( 375) hydrogen bonds : angle 2.42127 / 3.05 ( 703) *********************** 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 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.152 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0681 time to fit residues: 1.7824 Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 36 optimal weight: 50.0000 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 5.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 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 = 0.3997 r_free = 0.3997 target = 0.083947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047978 restraints weight = 50589.178| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.33 r_work: 0.2682 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11000 Z= 0.428 Angle : 0.844 26.536 16944 Z= 0.427 Chirality : 0.069 1.900 2221 Planarity : 0.006 0.040 581 Dihedral : 25.895 175.716 6645 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.04 % Allowed : 18.18 % Favored : 77.78 % 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: 0.58 (0.82), residues: 114 helix: 1.30 (0.75), residues: 48 sheet: -0.01 (0.84), residues: 26 loop : -0.31 (1.22), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.011 0.002 TYR B 94 PHE 0.020 0.003 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.43 (11000) covalent geometry : angle 0.84413 / 0.43 (16944) hydrogen bonds : bond 0.10978 / 11.96 ( 375) hydrogen bonds : angle 2.68533 / 3.39 ( 703) *********************** 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 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.107 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.0754 time to fit residues: 2.1745 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 91 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 40.0000 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 chunk 47 optimal weight: 0.5980 overall best weight: 3.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 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 = 0.4008 r_free = 0.4008 target = 0.084329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047443 restraints weight = 50649.511| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.09 r_work: 0.2699 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11000 Z= 0.309 Angle : 0.741 26.490 16944 Z= 0.386 Chirality : 0.063 1.910 2221 Planarity : 0.005 0.030 581 Dihedral : 25.897 175.695 6645 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.01 % Allowed : 23.23 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.85), residues: 114 helix: 1.59 (0.76), residues: 48 sheet: 0.23 (0.87), residues: 26 loop : -0.20 (1.26), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.009 0.002 TYR B 94 PHE 0.017 0.003 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.31 (11000) covalent geometry : angle 0.74078 / 0.39 (16944) hydrogen bonds : bond 0.09518 / 10.37 ( 375) hydrogen bonds : angle 2.50371 / 3.16 ( 703) *********************** 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 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.149 Fit side-chains REVERT: B 35 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7611 (mtp85) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0865 time to fit residues: 2.2752 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 15 optimal weight: 50.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.083045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.045846 restraints weight = 51137.622| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.97 r_work: 0.2696 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 11000 Z= 0.587 Angle : 1.025 26.755 16944 Z= 0.499 Chirality : 0.080 1.890 2221 Planarity : 0.007 0.046 581 Dihedral : 26.034 176.773 6645 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 28.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.81), residues: 114 helix: 0.83 (0.75), residues: 48 sheet: -0.06 (0.89), residues: 26 loop : -0.53 (1.16), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 62 TYR 0.012 0.003 TYR B 31 PHE 0.024 0.004 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00956 / 0.59 (11000) covalent geometry : angle 1.02505 / 0.50 (16944) hydrogen bonds : bond 0.12642 / 13.79 ( 375) hydrogen bonds : angle 2.93461 / 3.66 ( 703) *********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.146 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.0905 time to fit residues: 2.1681 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 91 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 chunk 7 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.083246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.047032 restraints weight = 50103.640| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.29 r_work: 0.2658 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11000 Z= 0.424 Angle : 0.869 26.825 16944 Z= 0.437 Chirality : 0.070 1.906 2221 Planarity : 0.006 0.036 581 Dihedral : 26.066 176.319 6645 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 1.01 % Allowed : 24.24 % Favored : 74.75 % 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: 0.33 (0.83), residues: 114 helix: 1.11 (0.77), residues: 48 sheet: -0.11 (0.89), residues: 26 loop : -0.51 (1.18), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.009 0.002 TYR B 81 PHE 0.021 0.004 PHE B 28 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.42 (11000) covalent geometry : angle 0.86934 / 0.44 (16944) hydrogen bonds : bond 0.10317 / 11.32 ( 375) hydrogen bonds : angle 2.70191 / 3.37 ( 703) *********************** 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 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.088 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.0644 time to fit residues: 1.5435 Evaluate side-chains 14 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 40.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 chunk 16 optimal weight: 50.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 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 = 0.3970 r_free = 0.3970 target = 0.082992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046532 restraints weight = 50136.264| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.23 r_work: 0.2669 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11000 Z= 0.415 Angle : 0.882 26.899 16944 Z= 0.443 Chirality : 0.071 1.896 2221 Planarity : 0.006 0.041 581 Dihedral : 26.046 176.544 6645 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 1.01 % Allowed : 24.24 % Favored : 74.75 % 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: 0.33 (0.82), residues: 114 helix: 1.13 (0.76), residues: 48 sheet: 0.10 (0.95), residues: 26 loop : -0.71 (1.13), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.010 0.002 TYR B 81 PHE 0.021 0.003 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.41 (11000) covalent geometry : angle 0.88180 / 0.44 (16944) hydrogen bonds : bond 0.11070 / 11.96 ( 375) hydrogen bonds : angle 2.74175 / 3.42 ( 703) ********************** 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 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.142 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.0670 time to fit residues: 1.4949 Evaluate side-chains 13 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 overall best weight: 5.0986 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.082946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.046485 restraints weight = 51085.926| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.28 r_work: 0.2662 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11000 Z= 0.395 Angle : 0.848 26.803 16944 Z= 0.429 Chirality : 0.069 1.903 2221 Planarity : 0.006 0.036 581 Dihedral : 26.042 176.300 6645 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 23.23 % Favored : 76.77 % 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 (0.84), residues: 114 helix: 1.29 (0.79), residues: 48 sheet: 0.05 (0.95), residues: 26 loop : -0.68 (1.14), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.009 0.003 TYR B 81 PHE 0.020 0.003 PHE B 28 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.39 (11000) covalent geometry : angle 0.84837 / 0.43 (16944) hydrogen bonds : bond 0.10286 / 11.21 ( 375) hydrogen bonds : angle 2.68442 / 3.37 ( 703) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4404.45 seconds wall clock time: 75 minutes 28.19 seconds (4528.19 seconds total)