Starting phenix.real_space_refine on Wed Aug 5 13:15:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zim_74279/08_2026/9zim_74279.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zim_74279/08_2026/9zim_74279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zim_74279/08_2026/9zim_74279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zim_74279/08_2026/9zim_74279.map" model { file = "/net/cci-nas-00/data/ceres_data/9zim_74279/08_2026/9zim_74279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zim_74279/08_2026/9zim_74279.cif" } resolution = 3.21 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 30 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 9940 Number of models: 1 Model: "" Number of chains: 5 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': 17, 'rna3p_pur': 218, 'rna3p_pyr': 157} Link IDs: {'rna2p': 42, 'rna3p': 374} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Unusual residues: {' MG': 29} Classifications: {'undetermined': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.26 Number of scatterers: 9940 At special positions: 0 Unit cell: (124.44, 168.36, 149.328, 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 30 11.99 O 3052 8.00 N 1834 7.00 C 4604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 72.3 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 44.8% alpha, 16.4% beta 137 base pairs and 218 stacking pairs defined. Time for finding SS restraints: 1.81 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 92 removed outlier: 3.563A pdb=" N GLU B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.629A pdb=" N LYS B 107 " --> pdb=" O HIS B 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.617A pdb=" N PHE B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B 42 " --> pdb=" O LYS B 79 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 218 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.13 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: 1044 1.33 - 1.45: 5245 1.45 - 1.57: 3873 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 151 " pdb=" C4 A A 151 " ideal model delta sigma weight residual 1.374 1.390 -0.016 6.00e-03 2.78e+04 6.78e+00 bond pdb=" N9 A A 148 " pdb=" C4 A A 148 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 3.02e+00 bond pdb=" C3' G A 32 " pdb=" O3' G A 32 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.20e-02 6.94e+03 2.56e+00 bond pdb=" N1 C A 207 " pdb=" C2 C A 207 " ideal model delta sigma weight residual 1.397 1.412 -0.015 1.00e-02 1.00e+04 2.13e+00 bond pdb=" C3' U A 264 " pdb=" O3' U A 264 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.20e-02 6.94e+03 2.05e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 15364 1.48 - 2.97: 1471 2.97 - 4.45: 84 4.45 - 5.94: 15 5.94 - 7.42: 10 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 118.00 3.90 7.00e-01 2.04e+00 3.11e+01 angle pdb=" C1' C A 207 " pdb=" N1 C A 207 " pdb=" C2 C A 207 " ideal model delta sigma weight residual 118.80 124.68 -5.88 1.10e+00 8.26e-01 2.86e+01 angle pdb=" C3' G A 32 " pdb=" O3' G A 32 " pdb=" P U A 33 " ideal model delta sigma weight residual 119.70 126.01 -6.31 1.20e+00 6.94e-01 2.76e+01 angle pdb=" C3' U A 264 " pdb=" O3' U A 264 " pdb=" P G A 265 " ideal model delta sigma weight residual 119.70 125.54 -5.84 1.20e+00 6.94e-01 2.37e+01 angle pdb=" C2' A A 151 " pdb=" C1' A A 151 " pdb=" N9 A A 151 " ideal model delta sigma weight residual 112.00 117.17 -5.17 1.10e+00 8.26e-01 2.21e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 5989 34.85 - 69.70: 984 69.70 - 104.55: 131 104.55 - 139.40: 4 139.40 - 174.26: 8 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" C4' G A 268 " pdb=" C3' G A 268 " pdb=" C2' G A 268 " pdb=" C1' G A 268 " ideal model delta sinusoidal sigma weight residual -35.00 31.01 -66.01 1 8.00e+00 1.56e-02 8.90e+01 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 40.72 159.28 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" C5' G A 268 " pdb=" C4' G A 268 " pdb=" C3' G A 268 " pdb=" O3' G A 268 " ideal model delta sinusoidal sigma weight residual 147.00 87.58 59.42 1 8.00e+00 1.56e-02 7.37e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1700 0.066 - 0.132: 321 0.132 - 0.198: 194 0.198 - 0.264: 4 0.264 - 0.330: 2 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C1' A A 151 " pdb=" O4' A A 151 " pdb=" C2' A A 151 " pdb=" N9 A A 151 " both_signs ideal model delta sigma weight residual False 2.47 2.14 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' G A 268 " pdb=" C4' G A 268 " pdb=" O3' G A 268 " pdb=" C2' G A 268 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' A A 50 " pdb=" O4' A A 50 " pdb=" C2' A A 50 " pdb=" N9 A A 50 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 50 " -0.030 2.00e-02 2.50e+03 1.39e-02 5.34e+00 pdb=" N9 A A 50 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A A 50 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 50 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 50 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 50 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A A 50 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 50 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A A 50 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 50 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 50 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.030 2.00e-02 2.50e+03 1.31e-02 5.14e+00 pdb=" N9 G A 298 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.001 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 " 0.002 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 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 397 " 0.029 2.00e-02 2.50e+03 1.44e-02 4.64e+00 pdb=" N1 U A 397 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U A 397 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U A 397 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 397 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U A 397 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U A 397 " 0.013 2.00e-02 2.50e+03 pdb=" C5 U A 397 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U A 397 " -0.007 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 37 2.53 - 3.12: 6860 3.12 - 3.71: 20818 3.71 - 4.31: 27552 4.31 - 4.90: 35050 Nonbonded interactions: 90317 Sorted by model distance: nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 510 " model vdw 1.932 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 510 " model vdw 1.948 2.170 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 510 " model vdw 1.960 2.170 nonbonded pdb=" OP2 G A 250 " pdb="MG MG A 518 " model vdw 1.985 2.170 nonbonded pdb=" OP2 A A 82 " pdb="MG MG A 518 " model vdw 1.986 2.170 ... (remaining 90312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.980 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: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.990 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 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 0.041 11000 Z= 0.262 Angle : 0.842 7.421 16944 Z= 0.703 Chirality : 0.064 0.330 2221 Planarity : 0.004 0.024 581 Dihedral : 25.320 174.255 6900 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.03 % Allowed : 33.33 % 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: 0.60 (0.82), residues: 114 helix: 2.34 (0.75), residues: 45 sheet: 1.34 (1.15), residues: 26 loop : -2.55 (0.85), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 59 TYR 0.010 0.002 TYR B 5 PHE 0.008 0.001 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.26 (11000) covalent geometry : angle 0.84218 / 0.70 (16944) hydrogen bonds : bond 0.08822 / 9.67 ( 398) hydrogen bonds : angle 3.62298 / 3.88 ( 735) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.098 Fit side-chains REVERT: B 11 GLU cc_start: 0.8897 (pt0) cc_final: 0.8624 (pm20) REVERT: B 70 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 96 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: B 113 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.6960 (tmtt) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.0756 time to fit residues: 2.8443 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 113 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.080443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048341 restraints weight = 60537.691| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.97 r_work: 0.2627 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 11000 Z= 0.573 Angle : 1.074 11.389 16944 Z= 0.538 Chirality : 0.076 0.499 2221 Planarity : 0.007 0.040 581 Dihedral : 25.671 169.959 6655 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 11.11 % Allowed : 21.21 % Favored : 67.68 % 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: -0.76 (0.79), residues: 114 helix: 1.46 (0.73), residues: 46 sheet: -0.45 (1.02), residues: 28 loop : -2.98 (0.91), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.040 0.004 TYR B 5 PHE 0.018 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.57 (11000) covalent geometry : angle 1.07405 / 0.54 (16944) hydrogen bonds : bond 0.14056 / 14.80 ( 398) hydrogen bonds : angle 3.21054 / 4.01 ( 735) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.100 Fit side-chains REVERT: B 38 GLN cc_start: 0.8363 (tt0) cc_final: 0.8127 (tt0) outliers start: 11 outliers final: 7 residues processed: 26 average time/residue: 0.0635 time to fit residues: 2.6162 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.080747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048705 restraints weight = 60831.739| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.56 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11000 Z= 0.348 Angle : 0.776 10.326 16944 Z= 0.409 Chirality : 0.056 0.439 2221 Planarity : 0.005 0.025 581 Dihedral : 25.755 167.460 6648 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.08 % Allowed : 20.20 % Favored : 71.72 % 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: -0.45 (0.78), residues: 114 helix: 1.89 (0.72), residues: 46 sheet: -0.06 (1.01), residues: 26 loop : -3.13 (0.84), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.025 0.003 TYR B 5 PHE 0.012 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.35 (11000) covalent geometry : angle 0.77642 / 0.41 (16944) hydrogen bonds : bond 0.10347 / 11.18 ( 398) hydrogen bonds : angle 2.76125 / 3.37 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.145 Fit side-chains REVERT: B 38 GLN cc_start: 0.8367 (tt0) cc_final: 0.8111 (tt0) REVERT: B 80 ASP cc_start: 0.8573 (m-30) cc_final: 0.8256 (m-30) REVERT: B 113 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8473 (mmtm) outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.0737 time to fit residues: 2.7434 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 50.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.080018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048210 restraints weight = 61342.121| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.64 r_work: 0.2647 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11000 Z= 0.370 Angle : 0.782 9.886 16944 Z= 0.416 Chirality : 0.056 0.432 2221 Planarity : 0.006 0.042 581 Dihedral : 25.835 167.755 6648 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 9.09 % Allowed : 18.18 % Favored : 72.73 % 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: -0.56 (0.78), residues: 114 helix: 1.99 (0.71), residues: 46 sheet: -0.44 (0.97), residues: 28 loop : -3.32 (0.84), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.026 0.003 TYR B 5 PHE 0.011 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.37 (11000) covalent geometry : angle 0.78181 / 0.42 (16944) hydrogen bonds : bond 0.10736 / 11.34 ( 398) hydrogen bonds : angle 2.73970 / 3.33 ( 735) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.161 Fit side-chains REVERT: B 113 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8233 (mmtm) outliers start: 9 outliers final: 7 residues processed: 25 average time/residue: 0.0878 time to fit residues: 3.3838 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.078103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.042164 restraints weight = 60569.255| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.44 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.099 11000 Z= 0.653 Angle : 1.239 13.708 16944 Z= 0.601 Chirality : 0.084 0.407 2221 Planarity : 0.008 0.039 581 Dihedral : 26.227 165.530 6648 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 37.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 11.11 % Allowed : 19.19 % 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: -1.90 (0.76), residues: 114 helix: 0.48 (0.71), residues: 48 sheet: -1.82 (0.88), residues: 31 loop : -3.09 (0.99), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.043 0.005 TYR B 5 PHE 0.014 0.003 PHE B 68 HIS 0.010 0.006 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01071 / 0.65 (11000) covalent geometry : angle 1.23868 / 0.60 (16944) hydrogen bonds : bond 0.15622 / 16.58 ( 398) hydrogen bonds : angle 3.32484 / 4.20 ( 735) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.148 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 26 average time/residue: 0.0828 time to fit residues: 3.3457 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 HIS ** 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 = 0.3903 r_free = 0.3903 target = 0.079303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043813 restraints weight = 60810.620| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.29 r_work: 0.2661 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11000 Z= 0.321 Angle : 0.773 11.184 16944 Z= 0.419 Chirality : 0.055 0.430 2221 Planarity : 0.006 0.029 581 Dihedral : 26.088 165.945 6648 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 7.07 % Allowed : 22.22 % Favored : 70.71 % 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 (0.78), residues: 114 helix: 1.75 (0.72), residues: 46 sheet: -1.33 (0.92), residues: 31 loop : -3.18 (0.92), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 26 TYR 0.025 0.003 TYR B 5 PHE 0.011 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.32 (11000) covalent geometry : angle 0.77329 / 0.42 (16944) hydrogen bonds : bond 0.11008 / 11.80 ( 398) hydrogen bonds : angle 2.76812 / 3.31 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.117 Fit side-chains REVERT: B 38 GLN cc_start: 0.8368 (tt0) cc_final: 0.8117 (tt0) outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.0601 time to fit residues: 2.2488 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 HIS ** 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 = 0.3888 r_free = 0.3888 target = 0.078629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.043776 restraints weight = 60130.741| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.53 r_work: 0.2638 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11000 Z= 0.428 Angle : 0.873 10.853 16944 Z= 0.456 Chirality : 0.061 0.419 2221 Planarity : 0.006 0.030 581 Dihedral : 26.080 165.041 6645 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 8.08 % Allowed : 24.24 % Favored : 67.68 % 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 (0.79), residues: 114 helix: 0.91 (0.73), residues: 52 sheet: -1.09 (0.91), residues: 29 loop : -3.00 (1.04), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.030 0.003 TYR B 5 PHE 0.010 0.002 PHE B 68 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.43 (11000) covalent geometry : angle 0.87270 / 0.46 (16944) hydrogen bonds : bond 0.12116 / 12.88 ( 398) hydrogen bonds : angle 2.93274 / 3.54 ( 735) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.091 Fit side-chains REVERT: B 38 GLN cc_start: 0.8400 (tt0) cc_final: 0.8094 (tt0) outliers start: 8 outliers final: 5 residues processed: 23 average time/residue: 0.0642 time to fit residues: 2.2904 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 91 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 50.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.077193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.041629 restraints weight = 59903.958| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.36 r_work: 0.2578 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.103 11000 Z= 0.668 Angle : 1.290 14.550 16944 Z= 0.624 Chirality : 0.086 0.432 2221 Planarity : 0.008 0.049 581 Dihedral : 26.464 164.843 6645 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 41.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 9.09 % Allowed : 25.25 % 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: -2.15 (0.75), residues: 114 helix: 0.03 (0.71), residues: 52 sheet: -1.94 (0.82), residues: 29 loop : -3.11 (1.00), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 62 TYR 0.042 0.005 TYR B 5 PHE 0.008 0.003 PHE B 17 HIS 0.012 0.008 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01086 / 0.67 (11000) covalent geometry : angle 1.29036 / 0.62 (16944) hydrogen bonds : bond 0.16919 / 17.94 ( 398) hydrogen bonds : angle 3.44318 / 4.29 ( 735) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.157 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 25 average time/residue: 0.0710 time to fit residues: 2.8454 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 17 optimal weight: 40.0000 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 HIS ** 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 = 0.3898 r_free = 0.3898 target = 0.078778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.043431 restraints weight = 60497.007| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.17 r_work: 0.2660 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11000 Z= 0.265 Angle : 0.739 11.095 16944 Z= 0.413 Chirality : 0.053 0.434 2221 Planarity : 0.006 0.032 581 Dihedral : 26.263 165.359 6645 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 6.06 % Allowed : 26.26 % Favored : 67.68 % 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: -1.03 (0.79), residues: 114 helix: 1.12 (0.72), residues: 52 sheet: -1.20 (0.89), residues: 29 loop : -3.10 (1.04), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.021 0.002 TYR B 5 PHE 0.008 0.001 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.27 (11000) covalent geometry : angle 0.73884 / 0.41 (16944) hydrogen bonds : bond 0.11212 / 12.04 ( 398) hydrogen bonds : angle 2.75593 / 3.27 ( 735) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.115 Fit side-chains REVERT: B 83 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.9004 (mm) outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 0.0554 time to fit residues: 2.0809 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 50.0000 chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 overall best weight: 6.3790 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.077943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.042891 restraints weight = 59909.244| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.56 r_work: 0.2631 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11000 Z= 0.460 Angle : 0.912 11.566 16944 Z= 0.474 Chirality : 0.065 0.415 2221 Planarity : 0.006 0.031 581 Dihedral : 26.234 164.942 6645 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 31.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 5.05 % Allowed : 29.29 % 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: -1.46 (0.77), residues: 114 helix: 0.77 (0.72), residues: 52 sheet: -1.52 (0.82), residues: 29 loop : -3.21 (1.04), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.030 0.004 TYR B 5 PHE 0.008 0.002 PHE B 68 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.46 (11000) covalent geometry : angle 0.91211 / 0.47 (16944) hydrogen bonds : bond 0.12726 / 13.54 ( 398) hydrogen bonds : angle 3.01095 / 3.64 ( 735) ********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.108 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 22 average time/residue: 0.0606 time to fit residues: 2.1058 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 41 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 0.1980 overall best weight: 4.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 HIS ** 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 = 0.3897 r_free = 0.3897 target = 0.078594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.043237 restraints weight = 60895.011| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.23 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11000 Z= 0.316 Angle : 0.758 10.865 16944 Z= 0.413 Chirality : 0.054 0.428 2221 Planarity : 0.006 0.031 581 Dihedral : 26.180 164.834 6645 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % 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: -1.05 (0.79), residues: 114 helix: 0.98 (0.72), residues: 52 sheet: -0.84 (0.88), residues: 26 loop : -3.11 (1.06), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.022 0.003 TYR B 5 PHE 0.011 0.001 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.32 (11000) covalent geometry : angle 0.75751 / 0.41 (16944) hydrogen bonds : bond 0.10731 / 11.49 ( 398) hydrogen bonds : angle 2.80162 / 3.33 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3684.45 seconds wall clock time: 63 minutes 32.49 seconds (3812.49 seconds total)