Starting phenix.real_space_refine on Wed Aug 5 13:16:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ziu_74284/08_2026/9ziu_74284.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ziu_74284/08_2026/9ziu_74284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ziu_74284/08_2026/9ziu_74284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ziu_74284/08_2026/9ziu_74284.map" model { file = "/net/cci-nas-00/data/ceres_data/9ziu_74284/08_2026/9ziu_74284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ziu_74284/08_2026/9ziu_74284.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 417 5.49 5 Mg 35 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 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9944 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': 30, 'rna2p_pyr': 15, 'rna3p_pur': 213, 'rna3p_pyr': 159} Link IDs: {'rna2p': 45, 'rna3p': 371} 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Unusual residues: {' MG': 35} Classifications: {'undetermined': 35} Link IDs: {None: 34} Time building chain proxies: 2.17, per 1000 atoms: 0.22 Number of scatterers: 9944 At special positions: 0 Unit cell: (94.428, 168.36, 150.06, 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 35 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: 0.59 Conformation dependent library (CDL) restraints added in 68.5 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 47.4% alpha, 11.2% beta 131 base pairs and 195 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.793A pdb=" N LEU B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 24 removed outlier: 3.602A pdb=" N LEU B 33 " --> pdb=" O ASP B 80 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 195 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 0.84 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: 1115 1.33 - 1.45: 5204 1.45 - 1.57: 3843 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 G A 32 " pdb=" C4 G A 32 " ideal model delta sigma weight residual 1.375 1.363 0.012 8.00e-03 1.56e+04 2.27e+00 bond pdb=" N7 A A 332 " pdb=" C5 A A 332 " ideal model delta sigma weight residual 1.388 1.379 0.009 6.00e-03 2.78e+04 2.23e+00 bond pdb=" N1 C A 129 " pdb=" C2 C A 129 " ideal model delta sigma weight residual 1.397 1.411 -0.014 1.00e-02 1.00e+04 2.06e+00 bond pdb=" C4' G A 230 " pdb=" O4' G A 230 " ideal model delta sigma weight residual 1.454 1.440 0.014 1.00e-02 1.00e+04 1.95e+00 bond pdb=" C2 G A 32 " pdb=" N3 G A 32 " ideal model delta sigma weight residual 1.323 1.312 0.011 8.00e-03 1.56e+04 1.89e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 15632 1.91 - 3.83: 1279 3.83 - 5.74: 28 5.74 - 7.65: 4 7.65 - 9.57: 1 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O2 C A 220 " pdb=" C2 C A 220 " pdb=" N3 C A 220 " ideal model delta sigma weight residual 121.90 117.70 4.20 7.00e-01 2.04e+00 3.60e+01 angle pdb=" C1' C A 245 " pdb=" N1 C A 245 " pdb=" C2 C A 245 " ideal model delta sigma weight residual 118.80 125.37 -6.57 1.10e+00 8.26e-01 3.56e+01 angle pdb=" N1 C A 220 " pdb=" C2 C A 220 " pdb=" O2 C A 220 " ideal model delta sigma weight residual 118.90 122.37 -3.47 6.00e-01 2.78e+00 3.34e+01 angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 118.10 3.80 7.00e-01 2.04e+00 2.94e+01 angle pdb=" C1' U A 222 " pdb=" N1 U A 222 " pdb=" C2 U A 222 " ideal model delta sigma weight residual 117.70 123.99 -6.29 1.20e+00 6.94e-01 2.75e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 5855 34.04 - 68.08: 1098 68.08 - 102.13: 150 102.13 - 136.17: 9 136.17 - 170.21: 4 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 37.32 162.68 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" C5' G A 230 " pdb=" C4' G A 230 " pdb=" C3' G A 230 " pdb=" O3' G A 230 " ideal model delta sinusoidal sigma weight residual 147.00 89.70 57.30 1 8.00e+00 1.56e-02 6.90e+01 dihedral pdb=" C4' G A 230 " pdb=" C3' G A 230 " pdb=" C2' G A 230 " pdb=" C1' G A 230 " ideal model delta sinusoidal sigma weight residual -35.00 21.30 -56.30 1 8.00e+00 1.56e-02 6.68e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1641 0.055 - 0.110: 184 0.110 - 0.165: 390 0.165 - 0.220: 5 0.220 - 0.274: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C1' G A 230 " pdb=" O4' G A 230 " pdb=" C2' G A 230 " pdb=" N9 G A 230 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' G A 237 " pdb=" C4' G A 237 " pdb=" O3' G A 237 " pdb=" C2' G A 237 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1' G A 213 " pdb=" O4' G A 213 " pdb=" C2' G A 213 " pdb=" N9 G A 213 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 230 " 0.032 2.00e-02 2.50e+03 1.40e-02 5.84e+00 pdb=" N9 G A 230 " -0.034 2.00e-02 2.50e+03 pdb=" C8 G A 230 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 230 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 230 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 230 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A 230 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G A 230 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 230 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 230 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 230 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 230 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.031 2.00e-02 2.50e+03 1.34e-02 5.42e+00 pdb=" N9 G A 298 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 298 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 220 " 0.023 2.00e-02 2.50e+03 1.40e-02 4.43e+00 pdb=" N1 C A 220 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C A 220 " 0.017 2.00e-02 2.50e+03 pdb=" O2 C A 220 " -0.014 2.00e-02 2.50e+03 pdb=" N3 C A 220 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A 220 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C A 220 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C A 220 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C A 220 " -0.008 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 45 2.52 - 3.11: 6927 3.11 - 3.71: 21063 3.71 - 4.30: 27530 4.30 - 4.90: 34997 Nonbonded interactions: 90562 Sorted by model distance: nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 509 " model vdw 1.921 2.170 nonbonded pdb=" N1 G A 298 " pdb="MG MG A 528 " model vdw 1.931 2.250 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 509 " model vdw 1.979 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 506 " model vdw 1.981 2.170 nonbonded pdb=" N1 G A 299 " pdb="MG MG A 528 " model vdw 2.005 2.250 ... (remaining 90557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.810 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 10.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 0.033 11000 Z= 0.263 Angle : 0.850 9.565 16944 Z= 0.731 Chirality : 0.063 0.274 2221 Planarity : 0.004 0.038 581 Dihedral : 26.291 170.211 6900 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 7.07 % Allowed : 36.36 % Favored : 56.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.80), residues: 114 helix: 2.30 (0.75), residues: 47 sheet: 0.07 (1.14), residues: 23 loop : -3.09 (0.75), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 26 TYR 0.008 0.001 TYR B 40 PHE 0.005 0.001 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.26 (11000) covalent geometry : angle 0.85024 / 0.73 (16944) hydrogen bonds : bond 0.09789 / 10.25 ( 376) hydrogen bonds : angle 3.00796 / 4.34 ( 682) *********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7559 (mtp85) cc_final: 0.6684 (mtm-85) REVERT: B 80 ASP cc_start: 0.8257 (m-30) cc_final: 0.7848 (m-30) outliers start: 7 outliers final: 7 residues processed: 32 average time/residue: 0.0991 time to fit residues: 4.3655 Evaluate side-chains 33 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.063560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037116 restraints weight = 75948.206| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.06 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 11000 Z= 0.551 Angle : 1.178 20.296 16944 Z= 0.575 Chirality : 0.079 0.487 2221 Planarity : 0.008 0.038 581 Dihedral : 26.863 172.295 6657 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 42.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 15.15 % Allowed : 26.26 % Favored : 58.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.76), residues: 114 helix: 0.59 (0.71), residues: 54 sheet: -0.69 (1.12), residues: 19 loop : -2.75 (0.84), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 59 TYR 0.016 0.004 TYR B 81 PHE 0.019 0.004 PHE B 28 HIS 0.009 0.006 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.55 (11000) covalent geometry : angle 1.17781 / 0.57 (16944) hydrogen bonds : bond 0.19871 / 20.35 ( 376) hydrogen bonds : angle 3.34936 / 4.45 ( 682) *********************** 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 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.140 Fit side-chains REVERT: B 3 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7259 (mtmm) REVERT: B 19 GLN cc_start: 0.9152 (mp10) cc_final: 0.8925 (mp10) REVERT: B 113 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6878 (mtmm) outliers start: 15 outliers final: 10 residues processed: 38 average time/residue: 0.0951 time to fit residues: 5.0059 Evaluate side-chains 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.063822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.037936 restraints weight = 76085.396| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.02 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11000 Z= 0.377 Angle : 0.866 10.431 16944 Z= 0.447 Chirality : 0.059 0.344 2221 Planarity : 0.006 0.036 581 Dihedral : 27.039 171.503 6652 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 32.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 15.15 % Allowed : 32.32 % Favored : 52.53 % 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: -1.02 (0.79), residues: 114 helix: 0.97 (0.74), residues: 54 sheet: -0.79 (1.25), residues: 19 loop : -2.95 (0.81), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 59 TYR 0.009 0.002 TYR B 31 PHE 0.015 0.002 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.38 (11000) covalent geometry : angle 0.86600 / 0.45 (16944) hydrogen bonds : bond 0.15250 / 15.33 ( 376) hydrogen bonds : angle 2.98476 / 3.96 ( 682) *********************** 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 45 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: B 3 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7293 (mtmm) REVERT: B 42 ARG cc_start: 0.7803 (mpp80) cc_final: 0.6748 (mtm180) REVERT: B 113 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6736 (mtmm) outliers start: 15 outliers final: 11 residues processed: 40 average time/residue: 0.0727 time to fit residues: 4.1694 Evaluate side-chains 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 100 SER 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 48 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.063834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037504 restraints weight = 76496.085| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.96 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11000 Z= 0.328 Angle : 0.756 9.243 16944 Z= 0.405 Chirality : 0.052 0.317 2221 Planarity : 0.006 0.035 581 Dihedral : 26.988 172.024 6652 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 28.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 14.14 % Allowed : 29.29 % Favored : 56.57 % 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: -1.08 (0.79), residues: 114 helix: 1.06 (0.77), residues: 54 sheet: -0.57 (1.14), residues: 17 loop : -3.25 (0.77), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.007 0.002 TYR B 40 PHE 0.022 0.003 PHE B 17 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.33 (11000) covalent geometry : angle 0.75633 / 0.40 (16944) hydrogen bonds : bond 0.14054 / 14.03 ( 376) hydrogen bonds : angle 2.96294 / 3.89 ( 682) *********************** 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 44 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: B 3 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7238 (mtmm) REVERT: B 13 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: B 42 ARG cc_start: 0.8005 (mpp80) cc_final: 0.6958 (mtm180) REVERT: B 79 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7624 (ptpp) REVERT: B 113 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6520 (mtpt) outliers start: 14 outliers final: 9 residues processed: 41 average time/residue: 0.0926 time to fit residues: 5.1647 Evaluate side-chains 43 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 111 LEU 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 18 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 19 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 0.0040 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 6.4000 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.063188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037562 restraints weight = 77064.833| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.29 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 11000 Z= 0.408 Angle : 0.883 10.079 16944 Z= 0.457 Chirality : 0.060 0.359 2221 Planarity : 0.006 0.033 581 Dihedral : 27.175 172.140 6649 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 36.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 16.16 % Allowed : 29.29 % Favored : 54.55 % 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: -1.57 (0.79), residues: 114 helix: 0.73 (0.74), residues: 54 sheet: -1.88 (1.00), residues: 26 loop : -3.19 (0.86), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 65 TYR 0.009 0.003 TYR B 31 PHE 0.016 0.003 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.41 (11000) covalent geometry : angle 0.88336 / 0.46 (16944) hydrogen bonds : bond 0.16576 / 16.72 ( 376) hydrogen bonds : angle 3.12281 / 4.05 ( 682) *********************** 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 44 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.113 Fit side-chains REVERT: B 42 ARG cc_start: 0.7581 (mpp80) cc_final: 0.6891 (mtm-85) REVERT: B 79 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7457 (ptpp) REVERT: B 106 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8351 (ttm-80) outliers start: 16 outliers final: 12 residues processed: 40 average time/residue: 0.1145 time to fit residues: 6.2246 Evaluate side-chains 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER 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 22 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.064008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.037844 restraints weight = 76750.233| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.76 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11000 Z= 0.227 Angle : 0.639 7.985 16944 Z= 0.361 Chirality : 0.043 0.308 2221 Planarity : 0.005 0.033 581 Dihedral : 27.053 172.507 6649 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 12.12 % Allowed : 34.34 % Favored : 53.54 % 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 (0.80), residues: 114 helix: 1.22 (0.76), residues: 54 sheet: -0.91 (1.04), residues: 19 loop : -2.95 (0.87), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 65 TYR 0.008 0.001 TYR B 94 PHE 0.021 0.002 PHE B 17 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.23 (11000) covalent geometry : angle 0.63936 / 0.36 (16944) hydrogen bonds : bond 0.12442 / 12.27 ( 376) hydrogen bonds : angle 2.83610 / 3.68 ( 682) *********************** 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 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.143 Fit side-chains REVERT: B 38 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: B 42 ARG cc_start: 0.7905 (mpp80) cc_final: 0.6911 (mtm180) REVERT: B 79 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7685 (ptpp) REVERT: B 80 ASP cc_start: 0.8309 (m-30) cc_final: 0.7851 (m-30) REVERT: B 107 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6416 (pttt) outliers start: 12 outliers final: 7 residues processed: 38 average time/residue: 0.0772 time to fit residues: 4.2324 Evaluate side-chains 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 107 LYS 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 22 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.062732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.036562 restraints weight = 78118.647| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.96 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 11000 Z= 0.505 Angle : 0.994 13.805 16944 Z= 0.495 Chirality : 0.067 0.450 2221 Planarity : 0.007 0.035 581 Dihedral : 27.254 172.782 6649 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 41.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 16.16 % Allowed : 29.29 % Favored : 54.55 % 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: -1.59 (0.76), residues: 114 helix: 0.74 (0.74), residues: 54 sheet: -1.47 (0.97), residues: 19 loop : -3.40 (0.79), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.008 0.002 TYR B 94 PHE 0.018 0.003 PHE B 17 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.51 (11000) covalent geometry : angle 0.99438 / 0.50 (16944) hydrogen bonds : bond 0.18056 / 18.27 ( 376) hydrogen bonds : angle 3.30236 / 4.22 ( 682) *********************** 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 45 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7523 (ptpp) REVERT: B 91 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: B 106 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8323 (ttm-80) outliers start: 16 outliers final: 11 residues processed: 40 average time/residue: 0.1049 time to fit residues: 5.7144 Evaluate side-chains 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.062752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036931 restraints weight = 77718.800| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.78 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 11000 Z= 0.464 Angle : 1.013 11.908 16944 Z= 0.513 Chirality : 0.069 0.514 2221 Planarity : 0.007 0.041 581 Dihedral : 27.597 172.905 6649 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 46.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 13.13 % Allowed : 34.34 % Favored : 52.53 % 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: -2.47 (0.74), residues: 114 helix: 0.34 (0.72), residues: 54 sheet: -3.04 (0.83), residues: 26 loop : -3.60 (0.79), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG B 42 TYR 0.015 0.003 TYR B 40 PHE 0.031 0.004 PHE B 17 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.46 (11000) covalent geometry : angle 1.01326 / 0.51 (16944) hydrogen bonds : bond 0.18702 / 18.84 ( 376) hydrogen bonds : angle 3.40933 / 4.36 ( 682) *********************** 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 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.142 Fit side-chains REVERT: B 79 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7653 (ptpp) REVERT: B 106 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8266 (ttm-80) REVERT: B 107 LYS cc_start: 0.7403 (pttt) cc_final: 0.6640 (pttt) outliers start: 13 outliers final: 11 residues processed: 39 average time/residue: 0.1062 time to fit residues: 5.8348 Evaluate side-chains 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER 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 13 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.063743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038463 restraints weight = 77079.255| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.86 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11000 Z= 0.226 Angle : 0.677 12.312 16944 Z= 0.381 Chirality : 0.046 0.382 2221 Planarity : 0.005 0.035 581 Dihedral : 27.353 174.068 6649 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 30.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 11.11 % Allowed : 35.35 % Favored : 53.54 % 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: -1.64 (0.76), residues: 114 helix: 0.65 (0.73), residues: 54 sheet: -1.35 (1.03), residues: 19 loop : -3.42 (0.81), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 42 TYR 0.011 0.002 TYR B 94 PHE 0.017 0.002 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.23 (11000) covalent geometry : angle 0.67686 / 0.38 (16944) hydrogen bonds : bond 0.13217 / 13.01 ( 376) hydrogen bonds : angle 2.92907 / 3.76 ( 682) *********************** 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 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.141 Fit side-chains REVERT: B 42 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7711 (mtp85) REVERT: B 106 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.8135 (ttm-80) outliers start: 11 outliers final: 8 residues processed: 36 average time/residue: 0.1202 time to fit residues: 5.8826 Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER 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 2 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 13 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.062230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036816 restraints weight = 77313.320| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.96 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 11000 Z= 0.570 Angle : 1.137 15.770 16944 Z= 0.554 Chirality : 0.076 0.521 2221 Planarity : 0.007 0.035 581 Dihedral : 27.510 173.833 6649 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 50.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 8.08 % Allowed : 36.36 % Favored : 55.56 % 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: -2.26 (0.74), residues: 114 helix: 0.23 (0.72), residues: 54 sheet: -1.70 (0.97), residues: 19 loop : -3.85 (0.74), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.015 0.003 TYR B 81 PHE 0.010 0.003 PHE B 28 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.57 (11000) covalent geometry : angle 1.13713 / 0.55 (16944) hydrogen bonds : bond 0.19983 / 20.27 ( 376) hydrogen bonds : angle 3.55036 / 4.48 ( 682) ********************** 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 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.154 Fit side-chains REVERT: B 91 GLU cc_start: 0.9148 (pt0) cc_final: 0.8665 (pp20) REVERT: B 106 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8263 (ttm-80) REVERT: B 107 LYS cc_start: 0.7363 (pttt) cc_final: 0.6607 (pttt) outliers start: 8 outliers final: 8 residues processed: 34 average time/residue: 0.0991 time to fit residues: 4.7316 Evaluate side-chains 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 100 SER 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 47 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 40.0000 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.064011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038793 restraints weight = 77665.902| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.77 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11000 Z= 0.178 Angle : 0.661 9.922 16944 Z= 0.373 Chirality : 0.044 0.362 2221 Planarity : 0.005 0.034 581 Dihedral : 27.329 174.652 6649 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 8.08 % Allowed : 36.36 % Favored : 55.56 % 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: -1.39 (0.80), residues: 114 helix: 0.84 (0.76), residues: 55 sheet: -1.62 (1.22), residues: 14 loop : -3.03 (0.82), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.008 0.001 TYR B 94 PHE 0.008 0.002 PHE B 17 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.18 (11000) covalent geometry : angle 0.66148 / 0.37 (16944) hydrogen bonds : bond 0.12424 / 12.20 ( 376) hydrogen bonds : angle 2.95003 / 3.68 ( 682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.34 seconds wall clock time: 37 minutes 42.38 seconds (2262.38 seconds total)