Starting phenix.real_space_refine on Wed Aug 5 13:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zij_74276/08_2026/9zij_74276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zij_74276/08_2026/9zij_74276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zij_74276/08_2026/9zij_74276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zij_74276/08_2026/9zij_74276.map" model { file = "/net/cci-nas-00/data/ceres_data/9zij_74276/08_2026/9zij_74276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zij_74276/08_2026/9zij_74276.cif" } resolution = 3.35 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 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': 35, 'rna2p_pyr': 23, 'rna3p_pur': 208, 'rna3p_pyr': 151} Link IDs: {'rna2p': 58, 'rna3p': 358} 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: 2.00, per 1000 atoms: 0.20 Number of scatterers: 9944 At special positions: 0 Unit cell: (93.696, 171.288, 142.008, 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: 0.71 Conformation dependent library (CDL) restraints added in 53.7 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, 14.7% beta 137 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 53 through 70 removed outlier: 3.558A pdb=" N ARG B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.531A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 47 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 0.96 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: 961 1.33 - 1.45: 5330 1.45 - 1.57: 3871 1.57 - 1.69: 833 1.69 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 170 " pdb=" C4 A A 170 " ideal model delta sigma weight residual 1.374 1.527 -0.153 6.00e-03 2.78e+04 6.48e+02 bond pdb=" N9 A A 170 " pdb=" C8 A A 170 " ideal model delta sigma weight residual 1.373 1.208 0.165 8.00e-03 1.56e+04 4.24e+02 bond pdb=" C8 A A 170 " pdb=" N7 A A 170 " ideal model delta sigma weight residual 1.311 1.424 -0.113 7.00e-03 2.04e+04 2.59e+02 bond pdb=" C5 A A 170 " pdb=" C4 A A 170 " ideal model delta sigma weight residual 1.383 1.298 0.085 7.00e-03 2.04e+04 1.47e+02 bond pdb=" N3 A A 170 " pdb=" C4 A A 170 " ideal model delta sigma weight residual 1.344 1.387 -0.043 6.00e-03 2.78e+04 5.13e+01 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.58: 16935 15.58 - 31.17: 5 31.17 - 46.75: 2 46.75 - 62.33: 0 62.33 - 77.92: 2 Bond angle restraints: 16944 Sorted by residual: angle pdb=" N9 A A 170 " pdb=" C8 A A 170 " pdb=" N7 A A 170 " ideal model delta sigma weight residual 113.80 35.88 77.92 5.00e-01 4.00e+00 2.43e+04 angle pdb=" N7 A A 170 " pdb=" C5 A A 170 " pdb=" C4 A A 170 " ideal model delta sigma weight residual 110.70 36.80 73.90 5.00e-01 4.00e+00 2.18e+04 angle pdb=" C8 A A 170 " pdb=" N9 A A 170 " pdb=" C4 A A 170 " ideal model delta sigma weight residual 105.80 60.90 44.90 4.00e-01 6.25e+00 1.26e+04 angle pdb=" C8 A A 170 " pdb=" N7 A A 170 " pdb=" C5 A A 170 " ideal model delta sigma weight residual 103.90 137.22 -33.32 5.00e-01 4.00e+00 4.44e+03 angle pdb=" N7 A A 170 " pdb=" C5 A A 170 " pdb=" C6 A A 170 " ideal model delta sigma weight residual 132.30 150.40 -18.10 7.00e-01 2.04e+00 6.68e+02 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 5929 34.54 - 69.09: 1033 69.09 - 103.63: 145 103.63 - 138.17: 6 138.17 - 172.72: 3 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 27.28 172.72 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A 347 " pdb=" C1' C A 347 " pdb=" N1 C A 347 " pdb=" C2 C A 347 " ideal model delta sinusoidal sigma weight residual -160.00 -50.22 -109.78 1 1.50e+01 4.44e-03 5.71e+01 dihedral pdb=" O4' C A 366 " pdb=" C1' C A 366 " pdb=" N1 C A 366 " pdb=" C2 C A 366 " ideal model delta sinusoidal sigma weight residual -160.00 -74.29 -85.71 1 1.50e+01 4.44e-03 3.95e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.400: 2220 0.400 - 0.799: 0 0.799 - 1.199: 0 1.199 - 1.599: 0 1.599 - 1.999: 1 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P A A 377 " pdb=" OP1 A A 377 " pdb=" OP2 A A 377 " pdb=" O5' A A 377 " both_signs ideal model delta sigma weight residual True 2.41 0.41 2.00 2.00e-01 2.50e+01 9.99e+01 chirality pdb=" CB ILE B 7 " pdb=" CA ILE B 7 " pdb=" CG1 ILE B 7 " pdb=" CG2 ILE B 7 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C3' A A 241 " pdb=" C4' A A 241 " pdb=" O3' A A 241 " pdb=" C2' A A 241 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 170 " 0.023 2.00e-02 2.50e+03 2.00e-02 1.10e+01 pdb=" N9 A A 170 " -0.053 2.00e-02 2.50e+03 pdb=" C8 A A 170 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A 170 " 0.029 2.00e-02 2.50e+03 pdb=" C5 A A 170 " -0.007 2.00e-02 2.50e+03 pdb=" C6 A A 170 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A A 170 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A A 170 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A A 170 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 170 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A A 170 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 173 " 0.019 2.00e-02 2.50e+03 1.56e-02 7.30e+00 pdb=" N9 G A 173 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G A 173 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G A 173 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 173 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 173 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G A 173 " 0.018 2.00e-02 2.50e+03 pdb=" N1 G A 173 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A 173 " -0.040 2.00e-02 2.50e+03 pdb=" N2 G A 173 " 0.019 2.00e-02 2.50e+03 pdb=" N3 G A 173 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G A 173 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 32 " -0.028 2.00e-02 2.50e+03 1.23e-02 4.56e+00 pdb=" N9 G A 32 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G A 32 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 32 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 32 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 32 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G A 32 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G A 32 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G A 32 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 32 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 32 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 32 " 0.003 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 42 2.47 - 3.07: 6026 3.07 - 3.68: 21124 3.68 - 4.29: 28222 4.29 - 4.90: 36039 Nonbonded interactions: 91453 Sorted by model distance: nonbonded pdb=" C8 A A 170 " pdb=" N3 A A 170 " model vdw 1.858 2.672 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 511 " model vdw 1.923 2.170 nonbonded pdb=" O4 U A 393 " pdb="MG MG A 534 " model vdw 1.931 2.170 nonbonded pdb=" OP2 C A 386 " pdb="MG MG A 501 " model vdw 1.938 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 512 " model vdw 1.948 2.170 ... (remaining 91448 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: 10.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.440 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.004 0.165 11000 Z= 0.486 Angle : 1.337 77.916 16944 Z= 2.092 Chirality : 0.077 1.999 2221 Planarity : 0.004 0.032 581 Dihedral : 25.687 172.717 6900 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.04 % Allowed : 33.33 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.82), residues: 114 helix: -0.57 (0.72), residues: 51 sheet: 1.35 (1.06), residues: 26 loop : -1.34 (1.13), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 57 TYR 0.007 0.001 TYR B 5 PHE 0.006 0.001 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.49 (11000) covalent geometry : angle 1.33655 / 2.09 (16944) hydrogen bonds : bond 0.09048 / 10.38 ( 397) hydrogen bonds : angle 3.62094 / 4.86 ( 724) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9226 (tptp) cc_final: 0.8814 (tptp) REVERT: B 92 MET cc_start: 0.6754 (ppp) cc_final: 0.5739 (ppp) REVERT: B 98 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7653 (ptpp) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.1101 time to fit residues: 4.3772 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain B residue 98 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: 7.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 overall best weight: 6.6988 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.064116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038512 restraints weight = 62694.005| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.25 r_work: 0.2653 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11000 Z= 0.431 Angle : 1.008 26.440 16944 Z= 0.491 Chirality : 0.078 1.895 2221 Planarity : 0.006 0.044 581 Dihedral : 25.900 171.848 6653 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 29.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 9.09 % Allowed : 28.28 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.79), residues: 114 helix: -1.47 (0.66), residues: 51 sheet: 1.29 (1.07), residues: 26 loop : -1.65 (1.08), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 6 TYR 0.013 0.002 TYR B 5 PHE 0.015 0.003 PHE B 41 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.43 (11000) covalent geometry : angle 1.00784 / 0.49 (16944) hydrogen bonds : bond 0.12386 / 12.97 ( 397) hydrogen bonds : angle 3.03048 / 4.28 ( 724) *********************** 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 38 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9244 (tptp) cc_final: 0.8866 (tptp) REVERT: B 59 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8497 (ttp-110) REVERT: B 98 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7470 (ttpp) outliers start: 9 outliers final: 3 residues processed: 36 average time/residue: 0.1365 time to fit residues: 6.5173 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 98 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.063325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037462 restraints weight = 62979.567| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.10 r_work: 0.2620 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11000 Z= 0.433 Angle : 1.006 25.141 16944 Z= 0.499 Chirality : 0.077 1.950 2221 Planarity : 0.007 0.038 581 Dihedral : 26.181 171.740 6651 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 11.11 % Allowed : 28.28 % Favored : 60.61 % 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: -2.76 (0.74), residues: 114 helix: -1.74 (0.71), residues: 45 sheet: -0.25 (0.92), residues: 29 loop : -3.01 (0.93), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 6 TYR 0.019 0.003 TYR B 31 PHE 0.012 0.002 PHE B 41 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.43 (11000) covalent geometry : angle 1.00635 / 0.50 (16944) hydrogen bonds : bond 0.12982 / 13.52 ( 397) hydrogen bonds : angle 3.33823 / 4.69 ( 724) *********************** 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 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.150 Fit side-chains REVERT: B 33 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5799 (mt) REVERT: B 50 LYS cc_start: 0.9137 (tptp) cc_final: 0.8817 (tptp) REVERT: B 59 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8554 (ttp-110) outliers start: 11 outliers final: 6 residues processed: 35 average time/residue: 0.1134 time to fit residues: 5.4029 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 overall best weight: 5.5590 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.063340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.037592 restraints weight = 62729.659| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.92 r_work: 0.2626 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11000 Z= 0.359 Angle : 0.892 25.670 16944 Z= 0.452 Chirality : 0.071 1.909 2221 Planarity : 0.006 0.027 581 Dihedral : 26.279 171.946 6647 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 29.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 12.12 % Allowed : 31.31 % 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: -2.59 (0.74), residues: 114 helix: -1.25 (0.75), residues: 45 sheet: -0.61 (0.87), residues: 29 loop : -3.00 (0.94), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 106 TYR 0.020 0.002 TYR B 94 PHE 0.013 0.003 PHE B 41 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.36 (11000) covalent geometry : angle 0.89217 / 0.45 (16944) hydrogen bonds : bond 0.12403 / 12.77 ( 397) hydrogen bonds : angle 3.16300 / 4.34 ( 724) *********************** 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 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.119 Fit side-chains REVERT: B 12 GLU cc_start: 0.9481 (mp0) cc_final: 0.8957 (pm20) REVERT: B 33 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5655 (mt) REVERT: B 50 LYS cc_start: 0.9102 (tptp) cc_final: 0.8823 (tptp) REVERT: B 59 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8583 (ttp-110) outliers start: 12 outliers final: 6 residues processed: 34 average time/residue: 0.1205 time to fit residues: 5.6700 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 0.0970 overall best weight: 6.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.062948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.037510 restraints weight = 62639.551| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.95 r_work: 0.2612 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11000 Z= 0.394 Angle : 0.955 25.740 16944 Z= 0.482 Chirality : 0.075 1.932 2221 Planarity : 0.006 0.031 581 Dihedral : 26.374 172.124 6647 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 33.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 17.17 % Allowed : 28.28 % 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: -3.07 (0.71), residues: 114 helix: -1.48 (0.69), residues: 45 sheet: -1.12 (0.82), residues: 29 loop : -3.26 (0.93), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 106 TYR 0.015 0.002 TYR B 5 PHE 0.014 0.003 PHE B 41 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.39 (11000) covalent geometry : angle 0.95477 / 0.48 (16944) hydrogen bonds : bond 0.13585 / 14.01 ( 397) hydrogen bonds : angle 3.32524 / 4.57 ( 724) *********************** 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 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.164 Fit side-chains REVERT: B 33 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5738 (mt) REVERT: B 50 LYS cc_start: 0.9110 (tptp) cc_final: 0.8841 (tptp) REVERT: B 59 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8625 (ttp-110) outliers start: 17 outliers final: 11 residues processed: 36 average time/residue: 0.1170 time to fit residues: 5.7790 Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 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 23 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 36 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.063246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.037492 restraints weight = 62501.724| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.84 r_work: 0.2615 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11000 Z= 0.325 Angle : 0.845 25.718 16944 Z= 0.435 Chirality : 0.070 1.927 2221 Planarity : 0.006 0.021 581 Dihedral : 26.365 172.064 6647 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 28.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 12.12 % Allowed : 29.29 % 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: -3.15 (0.67), residues: 114 helix: -1.37 (0.69), residues: 45 sheet: -1.44 (0.89), residues: 26 loop : -3.20 (0.77), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.016 0.002 TYR B 5 PHE 0.010 0.002 PHE B 41 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.32 (11000) covalent geometry : angle 0.84472 / 0.44 (16944) hydrogen bonds : bond 0.12397 / 12.64 ( 397) hydrogen bonds : angle 3.19987 / 4.36 ( 724) *********************** 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 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.139 Fit side-chains REVERT: B 12 GLU cc_start: 0.9502 (mp0) cc_final: 0.9009 (pm20) REVERT: B 33 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5687 (mt) REVERT: B 50 LYS cc_start: 0.9094 (tptp) cc_final: 0.8599 (tptp) REVERT: B 59 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8596 (ttp-110) outliers start: 12 outliers final: 10 residues processed: 31 average time/residue: 0.1247 time to fit residues: 5.3111 Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 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 23 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 40.0000 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.062287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.036679 restraints weight = 63636.325| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.79 r_work: 0.2571 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 11000 Z= 0.557 Angle : 1.169 26.155 16944 Z= 0.570 Chirality : 0.086 1.914 2221 Planarity : 0.008 0.038 581 Dihedral : 26.568 171.954 6646 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 42.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.30 % Favored : 80.70 % Rotamer: Outliers : 11.11 % Allowed : 30.30 % 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: -3.85 (0.66), residues: 114 helix: -2.15 (0.63), residues: 45 sheet: -1.58 (0.87), residues: 29 loop : -3.59 (0.82), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 57 TYR 0.021 0.002 TYR B 5 PHE 0.016 0.003 PHE B 41 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.56 (11000) covalent geometry : angle 1.16893 / 0.57 (16944) hydrogen bonds : bond 0.16642 / 17.07 ( 397) hydrogen bonds : angle 3.65734 / 5.01 ( 724) *********************** 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.150 Fit side-chains REVERT: B 59 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8585 (ttp-110) outliers start: 11 outliers final: 8 residues processed: 32 average time/residue: 0.1268 time to fit residues: 5.5464 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 103 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.062310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.036772 restraints weight = 63610.543| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.54 r_work: 0.2572 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11000 Z= 0.497 Angle : 1.097 26.073 16944 Z= 0.541 Chirality : 0.083 1.908 2221 Planarity : 0.007 0.023 581 Dihedral : 26.752 171.315 6646 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 38.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 14.14 % Allowed : 28.28 % Favored : 57.58 % 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: -4.08 (0.68), residues: 114 helix: -2.38 (0.60), residues: 45 sheet: -1.72 (0.88), residues: 29 loop : -3.64 (0.91), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.021 0.003 TYR B 5 PHE 0.016 0.003 PHE B 41 HIS 0.007 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.50 (11000) covalent geometry : angle 1.09724 / 0.54 (16944) hydrogen bonds : bond 0.15752 / 16.09 ( 397) hydrogen bonds : angle 3.67341 / 4.94 ( 724) *********************** 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 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.137 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 33 average time/residue: 0.1212 time to fit residues: 5.5122 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 103 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.063077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037520 restraints weight = 62340.971| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.69 r_work: 0.2618 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11000 Z= 0.258 Angle : 0.820 25.524 16944 Z= 0.431 Chirality : 0.068 1.938 2221 Planarity : 0.005 0.020 581 Dihedral : 26.626 172.152 6646 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 8.08 % Allowed : 31.31 % Favored : 60.61 % 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: -3.37 (0.71), residues: 114 helix: -1.64 (0.64), residues: 45 sheet: -1.31 (0.91), residues: 29 loop : -3.52 (0.93), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 57 TYR 0.015 0.002 TYR B 5 PHE 0.009 0.002 PHE B 41 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.26 (11000) covalent geometry : angle 0.81966 / 0.43 (16944) hydrogen bonds : bond 0.12526 / 12.80 ( 397) hydrogen bonds : angle 3.38919 / 4.54 ( 724) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.091 Fit side-chains REVERT: B 50 LYS cc_start: 0.9081 (tptp) cc_final: 0.8779 (tptp) outliers start: 8 outliers final: 8 residues processed: 26 average time/residue: 0.1237 time to fit residues: 4.2816 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 : 0.091 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 92 MET 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: 10.0000 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.061919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036555 restraints weight = 62870.573| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.80 r_work: 0.2559 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 11000 Z= 0.587 Angle : 1.220 26.286 16944 Z= 0.588 Chirality : 0.089 1.902 2221 Planarity : 0.008 0.039 581 Dihedral : 26.748 171.633 6646 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 43.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.18 % Favored : 79.82 % Rotamer: Outliers : 9.09 % Allowed : 32.32 % 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: -3.96 (0.69), residues: 114 helix: -2.05 (0.64), residues: 43 sheet: -1.70 (0.89), residues: 29 loop : -3.80 (0.87), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 57 TYR 0.025 0.003 TYR B 5 PHE 0.016 0.003 PHE B 41 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.59 (11000) covalent geometry : angle 1.22010 / 0.59 (16944) hydrogen bonds : bond 0.16683 / 17.06 ( 397) hydrogen bonds : angle 3.76510 / 5.11 ( 724) ********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.118 Fit side-chains REVERT: B 57 ARG cc_start: 0.8983 (mtp180) cc_final: 0.8584 (mtp85) outliers start: 9 outliers final: 9 residues processed: 26 average time/residue: 0.1140 time to fit residues: 4.0449 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 27 GLN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 103 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.063185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037706 restraints weight = 62825.475| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.50 r_work: 0.2625 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4402 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= 0.225 Angle : 0.793 25.522 16944 Z= 0.421 Chirality : 0.066 1.938 2221 Planarity : 0.005 0.029 581 Dihedral : 26.603 172.055 6646 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 8.08 % Allowed : 32.32 % Favored : 59.60 % 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: -3.21 (0.72), residues: 114 helix: -1.31 (0.68), residues: 45 sheet: -1.20 (0.91), residues: 29 loop : -3.70 (0.90), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.015 0.002 TYR B 5 PHE 0.011 0.002 PHE B 68 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.22 (11000) covalent geometry : angle 0.79286 / 0.42 (16944) hydrogen bonds : bond 0.12070 / 12.38 ( 397) hydrogen bonds : angle 3.35608 / 4.48 ( 724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.32 seconds wall clock time: 49 minutes 38.05 seconds (2978.05 seconds total)