Starting phenix.real_space_refine on Fri Sep 11 22:34:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owu_70944/09_2026/9owu_70944_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owu_70944/09_2026/9owu_70944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9owu_70944/09_2026/9owu_70944_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owu_70944/09_2026/9owu_70944_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9owu_70944/09_2026/9owu_70944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owu_70944/09_2026/9owu_70944.map" } resolution = 2.93 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 Ca 25 9.91 5 P 515 5.49 5 S 3 5.16 5 C 5530 2.51 5 N 2189 2.21 5 O 3749 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12011 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 15, 'rna3p_pur': 220, 'rna3p_pyr': 159} Link IDs: {'rna2p': 38, 'rna3p': 378} 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: "C" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1889 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 33, 'rna3p_pyr': 40} Link IDs: {'rna2p': 15, 'rna3p': 73} Chain: "E" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' CA': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 2.76, per 1000 atoms: 0.23 Number of scatterers: 12011 At special positions: 0 Unit cell: (125.453, 145.152, 163.814, 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) Ca 25 19.99 S 3 16.00 P 515 15.00 O 3749 8.00 N 2189 7.00 C 5530 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: 0.94 Conformation dependent library (CDL) restraints added in 197.6 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: 6 helices and 1 sheets defined 52.6% alpha, 16.4% beta 176 base pairs and 311 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix 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 removed outlier: 3.708A 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 removed outlier: 6.090A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 448 hydrogen bonds 766 hydrogen bond angles 0 basepair planarities 176 basepair parallelities 311 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1132 1.32 - 1.44: 6365 1.44 - 1.56: 4786 1.56 - 1.68: 1027 1.68 - 1.80: 5 Bond restraints: 13315 Sorted by residual: bond pdb=" CA SER B 48 " pdb=" CB SER B 48 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.55e-02 4.16e+03 1.66e+01 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.07e+01 bond pdb=" P C A 367 " pdb=" O5' C A 367 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.05e+01 bond pdb=" P C C -6 " pdb=" O5' C C -6 " ideal model delta sigma weight residual 1.593 1.624 -0.031 1.00e-02 1.00e+04 9.73e+00 bond pdb=" N LEU B 111 " pdb=" CA LEU B 111 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.19e-02 7.06e+03 9.50e+00 ... (remaining 13310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 18228 2.39 - 4.77: 1569 4.77 - 7.16: 707 7.16 - 9.55: 38 9.55 - 11.94: 4 Bond angle restraints: 20546 Sorted by residual: angle pdb=" C3' C C 69 " pdb=" C2' C C 69 " pdb=" C1' C C 69 " ideal model delta sigma weight residual 101.30 96.95 4.35 7.00e-01 2.04e+00 3.86e+01 angle pdb=" C4' C A 182 " pdb=" C3' C A 182 " pdb=" C2' C A 182 " ideal model delta sigma weight residual 102.60 96.75 5.85 1.00e+00 1.00e+00 3.43e+01 angle pdb=" C4' C C 69 " pdb=" C3' C C 69 " pdb=" C2' C C 69 " ideal model delta sigma weight residual 102.60 96.93 5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " ideal model delta sigma weight residual 108.50 112.32 -3.82 7.00e-01 2.04e+00 2.99e+01 angle pdb=" C3' A E -11 " pdb=" C2' A E -11 " pdb=" C1' A E -11 " ideal model delta sigma weight residual 101.30 97.56 3.74 7.00e-01 2.04e+00 2.85e+01 ... (remaining 20541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 7031 35.94 - 71.88: 1452 71.88 - 107.81: 179 107.81 - 143.75: 5 143.75 - 179.69: 9 Dihedral angle restraints: 8676 sinusoidal: 8339 harmonic: 337 Sorted by residual: dihedral pdb=" C4' U A 75 " pdb=" C3' U A 75 " pdb=" C2' U A 75 " pdb=" C1' U A 75 " ideal model delta sinusoidal sigma weight residual -35.00 31.01 -66.01 1 8.00e+00 1.56e-02 8.90e+01 dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 10.35 -170.35 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" C5' U A 75 " pdb=" C4' U A 75 " pdb=" C3' U A 75 " pdb=" O3' U A 75 " ideal model delta sinusoidal sigma weight residual 147.00 83.94 63.06 1 8.00e+00 1.56e-02 8.20e+01 ... (remaining 8673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1791 0.113 - 0.225: 535 0.225 - 0.338: 64 0.338 - 0.451: 245 0.451 - 0.563: 76 Chirality restraints: 2711 Sorted by residual: chirality pdb=" P C C -6 " pdb=" OP1 C C -6 " pdb=" OP2 C C -6 " pdb=" O5' C C -6 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" P C A 367 " pdb=" OP1 C A 367 " pdb=" OP2 C A 367 " pdb=" O5' C A 367 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.92e+00 chirality pdb=" P A C 75 " pdb=" OP1 A C 75 " pdb=" OP2 A C 75 " pdb=" O5' A C 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.88e+00 ... (remaining 2708 not shown) Planarity restraints: 679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " -0.414 9.50e-02 1.11e+02 1.86e-01 2.11e+01 pdb=" NE ARG B 59 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 299 " -0.050 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" N9 G A 299 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G A 299 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G A 299 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 299 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 299 " -0.018 2.00e-02 2.50e+03 pdb=" O6 G A 299 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G A 299 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G A 299 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G A 299 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A 299 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G A 299 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 318 " 0.033 2.00e-02 2.50e+03 1.64e-02 6.04e+00 pdb=" N1 C A 318 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C A 318 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C A 318 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C A 318 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A 318 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C A 318 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C A 318 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C A 318 " -0.010 2.00e-02 2.50e+03 ... (remaining 676 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 4 1.81 - 2.58: 182 2.58 - 3.36: 14555 3.36 - 4.13: 46378 4.13 - 4.90: 57069 Nonbonded interactions: 118188 Sorted by model distance: nonbonded pdb=" OP2 U A 293 " pdb="CA CA A 522 " model vdw 1.038 2.510 nonbonded pdb=" OP2 A A 364 " pdb=" C8 G A 365 " model vdw 1.337 3.260 nonbonded pdb=" O3' A A 363 " pdb=" C8 A A 364 " model vdw 1.361 3.260 nonbonded pdb=" C3' A A 363 " pdb=" C8 A A 364 " model vdw 1.367 3.690 nonbonded pdb=" OP2 A A 364 " pdb=" N9 G A 365 " model vdw 1.835 3.120 ... (remaining 118183 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.040 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.009 0.063 13315 Z= 0.713 Angle : 1.616 11.936 20546 Z= 0.960 Chirality : 0.171 0.563 2711 Planarity : 0.008 0.186 679 Dihedral : 27.830 179.688 8460 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % Favored : 66.67 % 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: 0.89 (0.81), residues: 114 helix: 1.32 (0.86), residues: 46 sheet: 0.92 (0.81), residues: 29 loop : -0.46 (1.06), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.010 0.001 TYR B 94 PHE 0.004 0.001 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00934 / 0.71 (13315) covalent geometry : angle 1.61587 / 0.96 (20546) hydrogen bonds : bond 0.20596 / 21.75 ( 497) hydrogen bonds : angle 9.27334 / 11.67 ( 895) *********************** 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 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.162 Fit side-chains REVERT: B 12 GLU cc_start: 0.8489 (mp0) cc_final: 0.7701 (mp0) REVERT: B 46 SER cc_start: 0.9060 (m) cc_final: 0.8757 (p) REVERT: B 63 TYR cc_start: 0.9128 (m-10) cc_final: 0.8855 (m-10) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 0.7099 time to fit residues: 29.7550 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.090387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.057262 restraints weight = 54864.052| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.33 r_work: 0.2858 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 13315 Z= 0.586 Angle : 1.086 11.765 20546 Z= 0.541 Chirality : 0.074 0.637 2711 Planarity : 0.008 0.052 679 Dihedral : 26.928 177.784 8208 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 9.09 % Allowed : 27.27 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.72), residues: 114 helix: 0.90 (0.66), residues: 48 sheet: 0.47 (0.71), residues: 29 loop : -0.22 (1.11), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 59 TYR 0.009 0.003 TYR B 31 PHE 0.008 0.002 PHE B 68 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00890 / 0.59 (13315) covalent geometry : angle 1.08597 / 0.54 (20546) hydrogen bonds : bond 0.13503 / 15.21 ( 497) hydrogen bonds : angle 3.29339 / 3.96 ( 895) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.170 Fit side-chains REVERT: B 6 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8729 (mtm180) REVERT: B 15 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 46 SER cc_start: 0.9237 (m) cc_final: 0.8529 (p) REVERT: B 111 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8357 (tm) outliers start: 9 outliers final: 3 residues processed: 25 average time/residue: 0.6549 time to fit residues: 17.7242 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 37 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.090565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.056927 restraints weight = 54703.815| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 0.99 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13315 Z= 0.345 Angle : 0.727 12.582 20546 Z= 0.395 Chirality : 0.049 0.681 2711 Planarity : 0.006 0.023 679 Dihedral : 26.833 176.868 8207 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 7.07 % Allowed : 27.27 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.77), residues: 114 helix: 1.28 (0.72), residues: 48 sheet: 0.11 (0.75), residues: 29 loop : -0.20 (1.20), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 59 TYR 0.009 0.003 TYR B 5 PHE 0.008 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.34 (13315) covalent geometry : angle 0.72698 / 0.39 (20546) hydrogen bonds : bond 0.09506 / 10.30 ( 497) hydrogen bonds : angle 2.77928 / 3.40 ( 895) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.166 Fit side-chains REVERT: B 6 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8639 (mtm180) REVERT: B 12 GLU cc_start: 0.8563 (mp0) cc_final: 0.7401 (mp0) REVERT: B 15 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 32 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 46 SER cc_start: 0.9060 (m) cc_final: 0.8314 (p) REVERT: B 111 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8621 (tm) outliers start: 7 outliers final: 2 residues processed: 25 average time/residue: 0.7533 time to fit residues: 20.2007 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 54 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 overall best weight: 4.2986 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.090556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.056934 restraints weight = 54357.017| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.46 r_work: 0.2901 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13315 Z= 0.419 Angle : 0.800 11.448 20546 Z= 0.421 Chirality : 0.057 0.567 2711 Planarity : 0.006 0.036 679 Dihedral : 26.661 176.848 8207 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 8.08 % Allowed : 29.29 % 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: 0.58 (0.79), residues: 114 helix: 1.07 (0.74), residues: 48 sheet: -0.20 (0.71), residues: 29 loop : 0.21 (1.26), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 86 TYR 0.010 0.002 TYR B 31 PHE 0.008 0.002 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.42 (13315) covalent geometry : angle 0.80043 / 0.42 (20546) hydrogen bonds : bond 0.10345 / 11.13 ( 497) hydrogen bonds : angle 2.71055 / 3.32 ( 895) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.169 Fit side-chains REVERT: B 6 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8781 (mtm180) REVERT: B 15 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 32 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8459 (p) REVERT: B 46 SER cc_start: 0.9220 (m) cc_final: 0.8474 (p) outliers start: 8 outliers final: 2 residues processed: 25 average time/residue: 0.8838 time to fit residues: 23.5096 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 50.0000 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.089851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.057054 restraints weight = 54815.304| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.42 r_work: 0.2890 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 13315 Z= 0.481 Angle : 0.878 12.003 20546 Z= 0.455 Chirality : 0.059 0.575 2711 Planarity : 0.006 0.028 679 Dihedral : 26.664 174.920 8207 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 11.11 % Allowed : 29.29 % 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: -0.25 (0.77), residues: 114 helix: 0.44 (0.74), residues: 48 sheet: -0.84 (0.69), residues: 29 loop : -0.09 (1.20), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 59 TYR 0.010 0.003 TYR B 31 PHE 0.014 0.003 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.48 (13315) covalent geometry : angle 0.87832 / 0.46 (20546) hydrogen bonds : bond 0.11341 / 12.25 ( 497) hydrogen bonds : angle 2.78772 / 3.39 ( 895) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.166 Fit side-chains REVERT: B 6 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8732 (mtm180) REVERT: B 15 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7756 (mt-10) REVERT: B 26 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8446 (ttp80) REVERT: B 32 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8482 (p) REVERT: B 46 SER cc_start: 0.9174 (m) cc_final: 0.8516 (p) REVERT: B 70 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8682 (mt-10) outliers start: 11 outliers final: 2 residues processed: 27 average time/residue: 0.8776 time to fit residues: 25.1874 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.089540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056601 restraints weight = 55794.235| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.34 r_work: 0.2914 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 13315 Z= 0.459 Angle : 0.826 11.563 20546 Z= 0.430 Chirality : 0.058 0.537 2711 Planarity : 0.006 0.062 679 Dihedral : 26.601 173.518 8205 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.06 % Allowed : 33.33 % 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: -0.39 (0.77), residues: 114 helix: 0.56 (0.74), residues: 48 sheet: -1.00 (0.66), residues: 29 loop : -0.46 (1.19), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 59 TYR 0.011 0.002 TYR B 31 PHE 0.009 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.46 (13315) covalent geometry : angle 0.82643 / 0.43 (20546) hydrogen bonds : bond 0.10418 / 11.08 ( 497) hydrogen bonds : angle 2.69550 / 3.28 ( 895) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.172 Fit side-chains REVERT: B 6 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8773 (mtm180) REVERT: B 15 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 32 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8395 (p) REVERT: B 46 SER cc_start: 0.9188 (m) cc_final: 0.8520 (p) outliers start: 6 outliers final: 1 residues processed: 24 average time/residue: 0.7856 time to fit residues: 20.1216 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.089755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.057282 restraints weight = 55443.564| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.14 r_work: 0.2924 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13315 Z= 0.372 Angle : 0.747 16.367 20546 Z= 0.397 Chirality : 0.051 0.529 2711 Planarity : 0.006 0.027 679 Dihedral : 26.530 173.137 8205 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.05 % Allowed : 34.34 % 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: -0.37 (0.79), residues: 114 helix: 0.72 (0.76), residues: 48 sheet: -1.45 (0.67), residues: 31 loop : -0.11 (1.25), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 59 TYR 0.010 0.002 TYR B 31 PHE 0.011 0.002 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.37 (13315) covalent geometry : angle 0.74713 / 0.40 (20546) hydrogen bonds : bond 0.09700 / 10.35 ( 497) hydrogen bonds : angle 2.62967 / 3.17 ( 895) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.160 Fit side-chains REVERT: B 6 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8770 (mtm180) REVERT: B 15 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 32 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 46 SER cc_start: 0.9188 (m) cc_final: 0.8531 (p) outliers start: 5 outliers final: 1 residues processed: 22 average time/residue: 0.8371 time to fit residues: 19.7172 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.089604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.056958 restraints weight = 55558.315| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.21 r_work: 0.2913 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13315 Z= 0.422 Angle : 0.815 11.800 20546 Z= 0.423 Chirality : 0.056 0.535 2711 Planarity : 0.006 0.057 679 Dihedral : 26.495 173.356 8205 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.06 % Allowed : 34.34 % 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: -0.38 (0.78), residues: 114 helix: 0.78 (0.75), residues: 48 sheet: -1.27 (0.65), residues: 29 loop : -0.51 (1.20), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 59 TYR 0.015 0.002 TYR B 5 PHE 0.010 0.002 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.42 (13315) covalent geometry : angle 0.81451 / 0.42 (20546) hydrogen bonds : bond 0.10436 / 11.11 ( 497) hydrogen bonds : angle 2.71045 / 3.24 ( 895) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.159 Fit side-chains REVERT: B 6 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8812 (mtm180) REVERT: B 15 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 32 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8422 (p) REVERT: B 46 SER cc_start: 0.9184 (m) cc_final: 0.8522 (p) outliers start: 6 outliers final: 2 residues processed: 23 average time/residue: 0.8224 time to fit residues: 20.1798 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.089865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057775 restraints weight = 55517.139| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.34 r_work: 0.2905 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13315 Z= 0.402 Angle : 0.765 11.805 20546 Z= 0.403 Chirality : 0.053 0.521 2711 Planarity : 0.006 0.037 679 Dihedral : 26.473 173.676 8205 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 36.36 % 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: -0.19 (0.79), residues: 114 helix: 1.02 (0.78), residues: 47 sheet: -1.05 (0.62), residues: 26 loop : -0.67 (1.13), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 59 TYR 0.009 0.002 TYR B 31 PHE 0.020 0.003 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.40 (13315) covalent geometry : angle 0.76546 / 0.40 (20546) hydrogen bonds : bond 0.09687 / 10.28 ( 497) hydrogen bonds : angle 2.65962 / 3.20 ( 895) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.166 Fit side-chains REVERT: B 6 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8833 (mtm180) REVERT: B 15 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 32 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8381 (p) REVERT: B 46 SER cc_start: 0.9200 (m) cc_final: 0.8526 (p) outliers start: 5 outliers final: 2 residues processed: 21 average time/residue: 0.8436 time to fit residues: 18.9297 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.090214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057431 restraints weight = 56108.942| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 0.94 r_work: 0.2940 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13315 Z= 0.269 Angle : 0.631 11.878 20546 Z= 0.350 Chirality : 0.044 0.486 2711 Planarity : 0.005 0.046 679 Dihedral : 26.398 173.667 8205 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.03 % Allowed : 38.38 % 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: 0.02 (0.81), residues: 114 helix: 1.28 (0.79), residues: 47 sheet: -1.31 (0.71), residues: 28 loop : -0.32 (1.17), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 59 TYR 0.009 0.001 TYR B 31 PHE 0.011 0.002 PHE B 28 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.27 (13315) covalent geometry : angle 0.63066 / 0.35 (20546) hydrogen bonds : bond 0.08470 / 8.93 ( 497) hydrogen bonds : angle 2.52619 / 3.07 ( 895) ********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.167 Fit side-chains REVERT: B 12 GLU cc_start: 0.8627 (mp0) cc_final: 0.7619 (mp0) REVERT: B 15 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 32 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8380 (p) outliers start: 3 outliers final: 1 residues processed: 24 average time/residue: 0.8028 time to fit residues: 20.5648 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 52 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.088460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055800 restraints weight = 55626.495| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.97 r_work: 0.2875 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.090 13315 Z= 0.677 Angle : 1.086 12.737 20546 Z= 0.528 Chirality : 0.074 0.551 2711 Planarity : 0.007 0.043 679 Dihedral : 26.450 177.716 8205 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.02 % Allowed : 39.39 % 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: -0.70 (0.77), residues: 114 helix: 0.52 (0.76), residues: 47 sheet: -1.29 (0.63), residues: 26 loop : -0.86 (1.10), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 59 TYR 0.011 0.003 TYR B 31 PHE 0.014 0.003 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01040 / 0.68 (13315) covalent geometry : angle 1.08641 / 0.53 (20546) hydrogen bonds : bond 0.13094 / 14.04 ( 497) hydrogen bonds : angle 2.95455 / 3.52 ( 895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5071.86 seconds wall clock time: 87 minutes 12.84 seconds (5232.84 seconds total)