Starting phenix.real_space_refine on Thu Jun 4 02:32:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zic_74269/06_2026/9zic_74269.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zic_74269/06_2026/9zic_74269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zic_74269/06_2026/9zic_74269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zic_74269/06_2026/9zic_74269.map" model { file = "/net/cci-nas-00/data/ceres_data/9zic_74269/06_2026/9zic_74269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zic_74269/06_2026/9zic_74269.cif" } resolution = 3.2 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 24 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 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9933 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': 25, 'rna2p_pyr': 15, 'rna3p_pur': 218, 'rna3p_pyr': 159} Link IDs: {'rna2p': 40, 'rna3p': 376} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Unusual residues: {' MG': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Time building chain proxies: 2.28, per 1000 atoms: 0.23 Number of scatterers: 9933 At special positions: 0 Unit cell: (125.172, 166.896, 147.864, 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 24 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: 0.77 Conformation dependent library (CDL) restraints added in 65.0 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 44.0% alpha, 17.2% beta 139 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... 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 90 Processing helix chain 'B' and resid 93 through 109 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.511A pdb=" N VAL B 21 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 2.25 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: 1093 1.33 - 1.45: 5296 1.45 - 1.57: 3773 1.57 - 1.69: 833 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" CB GLU B 96 " pdb=" CG GLU B 96 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" C3' U A 126 " pdb=" O3' U A 126 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.19e+00 bond pdb=" CB GLU B 37 " pdb=" CG GLU B 37 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CB GLU B 91 " pdb=" CG GLU B 91 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 1.468 1.457 0.011 1.24e-02 6.50e+03 8.46e-01 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 16932 5.40 - 10.79: 9 10.79 - 16.19: 1 16.19 - 21.58: 0 21.58 - 26.98: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O3' G A 114 " pdb=" P C A 115 " pdb=" OP1 C A 115 " ideal model delta sigma weight residual 108.00 81.02 26.98 3.00e+00 1.11e-01 8.09e+01 angle pdb=" O3' G A 114 " pdb=" P C A 115 " pdb=" OP2 C A 115 " ideal model delta sigma weight residual 108.00 83.36 24.64 3.00e+00 1.11e-01 6.74e+01 angle pdb=" C2' A A 195 " pdb=" C1' A A 195 " pdb=" N9 A A 195 " ideal model delta sigma weight residual 112.00 118.94 -6.94 1.50e+00 4.44e-01 2.14e+01 angle pdb=" CA GLU B 96 " pdb=" CB GLU B 96 " pdb=" CG GLU B 96 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" OP1 C A 115 " pdb=" P C A 115 " pdb=" OP2 C A 115 " ideal model delta sigma weight residual 119.60 130.60 -11.00 3.00e+00 1.11e-01 1.34e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 5986 35.85 - 71.70: 989 71.70 - 107.55: 133 107.55 - 143.40: 3 143.40 - 179.25: 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 200.00 30.72 169.28 1 1.50e+01 4.44e-03 8.46e+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 -42.67 -117.33 1 1.50e+01 4.44e-03 6.23e+01 dihedral pdb=" O4' U A 34 " pdb=" C1' U A 34 " pdb=" N1 U A 34 " pdb=" C2 U A 34 " ideal model delta sinusoidal sigma weight residual -160.00 -57.51 -102.49 1 1.50e+01 4.44e-03 5.19e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.387: 2220 0.387 - 0.774: 0 0.774 - 1.161: 0 1.161 - 1.548: 0 1.548 - 1.935: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P C A 115 " pdb=" OP1 C A 115 " pdb=" OP2 C A 115 " pdb=" O5' C A 115 " both_signs ideal model delta sigma weight residual True 2.41 0.47 1.94 2.00e-01 2.50e+01 9.37e+01 chirality pdb=" C1' A A 195 " pdb=" O4' A A 195 " pdb=" C2' A A 195 " pdb=" N9 A A 195 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' A A 146 " pdb=" C4' A A 146 " pdb=" O3' A A 146 " pdb=" C2' A A 146 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 195 " -0.070 2.00e-02 2.50e+03 3.19e-02 2.80e+01 pdb=" N9 A A 195 " 0.075 2.00e-02 2.50e+03 pdb=" C8 A A 195 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 195 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 195 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 195 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A A 195 " -0.019 2.00e-02 2.50e+03 pdb=" N1 A A 195 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A A 195 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A A 195 " 0.013 2.00e-02 2.50e+03 pdb=" C4 A A 195 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.034 2.00e-02 2.50e+03 1.50e-02 6.72e+00 pdb=" N9 G A 298 " -0.037 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 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' A A 232 " 0.024 2.00e-02 2.50e+03 1.54e-02 6.54e+00 pdb=" N9 A A 232 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A A 232 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A A 232 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A A 232 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A 232 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A A 232 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A A 232 " -0.020 2.00e-02 2.50e+03 pdb=" C2 A A 232 " 0.015 2.00e-02 2.50e+03 pdb=" N3 A A 232 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A A 232 " -0.001 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 44 2.54 - 3.13: 7098 3.13 - 3.72: 20971 3.72 - 4.31: 27681 4.31 - 4.90: 34789 Nonbonded interactions: 90583 Sorted by model distance: nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 508 " model vdw 1.953 2.170 nonbonded pdb=" OP2 A A 82 " pdb="MG MG A 518 " model vdw 1.987 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 509 " model vdw 2.001 2.170 nonbonded pdb=" OP2 G A 288 " pdb="MG MG A 517 " model vdw 2.002 2.170 nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 506 " model vdw 2.006 2.170 ... (remaining 90578 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: 8.490 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 11.360 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 0.034 11000 Z= 0.142 Angle : 0.633 26.976 16944 Z= 0.308 Chirality : 0.051 1.935 2221 Planarity : 0.004 0.032 581 Dihedral : 25.627 179.247 6900 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 35.35 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.85), residues: 114 helix: 2.31 (0.80), residues: 46 sheet: 0.84 (1.05), residues: 26 loop : -1.83 (1.00), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.009 0.002 TYR B 31 PHE 0.008 0.001 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (11000) covalent geometry : angle 0.63291 / 0.31 (16944) hydrogen bonds : bond 0.10413 / 6.02 ( 400) hydrogen bonds : angle 3.77819 / 2.02 ( 749) *********************** 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 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0625 time to fit residues: 1.7849 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 : 0.129 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 0.0870 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.086280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047316 restraints weight = 60033.392| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.60 r_work: 0.2697 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11000 Z= 0.332 Angle : 0.721 26.923 16944 Z= 0.347 Chirality : 0.054 1.921 2221 Planarity : 0.004 0.020 581 Dihedral : 25.852 179.200 6645 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.04 % Allowed : 32.32 % Favored : 63.64 % 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: 0.63 (0.84), residues: 114 helix: 2.01 (0.77), residues: 48 sheet: 0.75 (1.06), residues: 26 loop : -1.90 (1.04), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 106 TYR 0.013 0.002 TYR B 31 PHE 0.016 0.002 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.33 (11000) covalent geometry : angle 0.72060 / 0.35 (16944) hydrogen bonds : bond 0.07805 / 4.57 ( 400) hydrogen bonds : angle 2.34539 / 1.43 ( 749) *********************** 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 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.121 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.1024 time to fit residues: 2.7212 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.085651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.046148 restraints weight = 60092.993| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.49 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2397 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= 0.307 Angle : 0.711 27.052 16944 Z= 0.341 Chirality : 0.054 1.916 2221 Planarity : 0.004 0.019 581 Dihedral : 25.926 176.622 6645 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.05 % Allowed : 26.26 % Favored : 68.69 % 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: 0.87 (0.86), residues: 114 helix: 2.16 (0.77), residues: 48 sheet: 0.92 (1.11), residues: 26 loop : -1.73 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.012 0.002 TYR B 40 PHE 0.012 0.002 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.31 (11000) covalent geometry : angle 0.71149 / 0.34 (16944) hydrogen bonds : bond 0.07257 / 4.27 ( 400) hydrogen bonds : angle 2.32101 / 1.43 ( 749) *********************** 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.143 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 19 average time/residue: 0.0813 time to fit residues: 2.3827 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 50.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.084618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.045274 restraints weight = 60028.738| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.79 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11000 Z= 0.388 Angle : 0.778 26.866 16944 Z= 0.372 Chirality : 0.056 1.915 2221 Planarity : 0.005 0.024 581 Dihedral : 26.069 177.501 6645 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.06 % Allowed : 25.25 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.85), residues: 114 helix: 1.97 (0.76), residues: 48 sheet: 0.72 (1.11), residues: 26 loop : -1.76 (1.06), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.014 0.002 TYR B 40 PHE 0.015 0.002 PHE B 13 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.39 (11000) covalent geometry : angle 0.77781 / 0.37 (16944) hydrogen bonds : bond 0.08618 / 5.01 ( 400) hydrogen bonds : angle 2.49160 / 1.52 ( 749) *********************** 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 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.090 Fit side-chains REVERT: B 92 MET cc_start: 0.8894 (ttt) cc_final: 0.8463 (ttt) outliers start: 6 outliers final: 5 residues processed: 18 average time/residue: 0.0959 time to fit residues: 2.5730 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.086584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047203 restraints weight = 60184.280| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.17 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11000 Z= 0.177 Angle : 0.650 27.027 16944 Z= 0.309 Chirality : 0.052 1.931 2221 Planarity : 0.004 0.026 581 Dihedral : 25.805 174.795 6645 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.04 % Allowed : 27.27 % Favored : 68.69 % 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: 1.33 (0.88), residues: 114 helix: 2.40 (0.77), residues: 48 sheet: 1.43 (1.19), residues: 26 loop : -1.52 (1.11), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.010 0.001 TYR B 31 PHE 0.005 0.001 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 (11000) covalent geometry : angle 0.65019 / 0.31 (16944) hydrogen bonds : bond 0.06186 / 3.71 ( 400) hydrogen bonds : angle 2.27534 / 1.38 ( 749) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.150 Fit side-chains REVERT: B 19 GLN cc_start: 0.8454 (mp10) cc_final: 0.8218 (mp10) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.0759 time to fit residues: 2.5698 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 : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 41 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.084846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.045562 restraints weight = 60042.338| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.71 r_work: 0.2657 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11000 Z= 0.350 Angle : 0.741 26.832 16944 Z= 0.354 Chirality : 0.054 1.920 2221 Planarity : 0.004 0.021 581 Dihedral : 25.962 177.410 6645 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.06 % Allowed : 28.28 % Favored : 65.66 % 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: 0.86 (0.85), residues: 114 helix: 2.09 (0.76), residues: 48 sheet: 0.85 (1.12), residues: 26 loop : -1.59 (1.07), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.012 0.002 TYR B 40 PHE 0.014 0.002 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.35 (11000) covalent geometry : angle 0.74102 / 0.35 (16944) hydrogen bonds : bond 0.07980 / 4.67 ( 400) hydrogen bonds : angle 2.48269 / 1.52 ( 749) *********************** 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.163 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 19 average time/residue: 0.0752 time to fit residues: 2.3169 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.085044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045332 restraints weight = 59777.775| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.42 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11000 Z= 0.307 Angle : 0.716 26.961 16944 Z= 0.342 Chirality : 0.054 1.917 2221 Planarity : 0.004 0.022 581 Dihedral : 25.952 176.867 6645 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 30.30 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.86), residues: 114 helix: 2.10 (0.75), residues: 48 sheet: 1.00 (1.16), residues: 26 loop : -1.45 (1.09), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.012 0.002 TYR B 40 PHE 0.011 0.002 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.31 (11000) covalent geometry : angle 0.71639 / 0.34 (16944) hydrogen bonds : bond 0.07323 / 4.31 ( 400) hydrogen bonds : angle 2.49079 / 1.52 ( 749) *********************** 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.146 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 18 average time/residue: 0.0767 time to fit residues: 2.2651 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.083190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044731 restraints weight = 59668.562| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.59 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 11000 Z= 0.541 Angle : 0.902 27.049 16944 Z= 0.431 Chirality : 0.059 1.899 2221 Planarity : 0.005 0.032 581 Dihedral : 26.291 179.191 6645 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 6.06 % Allowed : 30.30 % Favored : 63.64 % 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: 0.39 (0.85), residues: 114 helix: 1.28 (0.72), residues: 54 sheet: 0.51 (1.11), residues: 26 loop : -1.59 (1.23), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.018 0.002 TYR B 40 PHE 0.016 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01027 / 0.54 (11000) covalent geometry : angle 0.90180 / 0.43 (16944) hydrogen bonds : bond 0.10742 / 6.19 ( 400) hydrogen bonds : angle 2.83571 / 1.73 ( 749) *********************** 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 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.101 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 17 average time/residue: 0.0665 time to fit residues: 1.8470 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.085148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.046634 restraints weight = 59901.200| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.32 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11000 Z= 0.227 Angle : 0.693 27.167 16944 Z= 0.330 Chirality : 0.053 1.917 2221 Planarity : 0.004 0.019 581 Dihedral : 26.023 176.654 6645 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % 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: 0.97 (0.86), residues: 114 helix: 2.14 (0.76), residues: 48 sheet: 1.02 (1.15), residues: 26 loop : -1.57 (1.08), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.010 0.002 TYR B 94 PHE 0.008 0.001 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.23 (11000) covalent geometry : angle 0.69342 / 0.33 (16944) hydrogen bonds : bond 0.06635 / 3.93 ( 400) hydrogen bonds : angle 2.51280 / 1.53 ( 749) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.101 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 20 average time/residue: 0.0686 time to fit residues: 2.2551 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.0370 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.084987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.046042 restraints weight = 59026.278| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.24 r_work: 0.2687 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11000 Z= 0.260 Angle : 0.696 26.959 16944 Z= 0.331 Chirality : 0.053 1.925 2221 Planarity : 0.004 0.023 581 Dihedral : 25.989 177.887 6645 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 5.05 % Allowed : 31.31 % Favored : 63.64 % 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: 0.99 (0.86), residues: 114 helix: 2.04 (0.76), residues: 48 sheet: 1.02 (1.16), residues: 26 loop : -1.36 (1.10), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.010 0.002 TYR B 31 PHE 0.009 0.001 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.26 (11000) covalent geometry : angle 0.69569 / 0.33 (16944) hydrogen bonds : bond 0.07094 / 4.18 ( 400) hydrogen bonds : angle 2.55575 / 1.55 ( 749) ********************** 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 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.093 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 18 average time/residue: 0.0711 time to fit residues: 2.0607 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.085110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.046335 restraints weight = 59798.492| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.20 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3828 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= 0.241 Angle : 0.691 26.953 16944 Z= 0.329 Chirality : 0.052 1.927 2221 Planarity : 0.004 0.019 581 Dihedral : 25.985 177.844 6645 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 4.04 % Allowed : 33.33 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.87), residues: 114 helix: 2.06 (0.76), residues: 48 sheet: 1.06 (1.16), residues: 26 loop : -1.27 (1.11), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.010 0.002 TYR B 31 PHE 0.009 0.001 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.24 (11000) covalent geometry : angle 0.69067 / 0.33 (16944) hydrogen bonds : bond 0.06947 / 4.10 ( 400) hydrogen bonds : angle 2.47495 / 1.52 ( 749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3779.52 seconds wall clock time: 65 minutes 7.62 seconds (3907.62 seconds total)