Starting phenix.real_space_refine on Fri Jul 3 04:11:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owt_70943/07_2026/9owt_70943_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owt_70943/07_2026/9owt_70943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9owt_70943/07_2026/9owt_70943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owt_70943/07_2026/9owt_70943.map" model { file = "/net/cci-nas-00/data/ceres_data/9owt_70943/07_2026/9owt_70943_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owt_70943/07_2026/9owt_70943_neut.cif" } resolution = 2.82 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 Ca 29 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12015 Number of models: 1 Model: "" Number of chains: 6 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': 14, 'rna3p_pur': 220, 'rna3p_pyr': 160} Link IDs: {'rna2p': 37, 'rna3p': 379} 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': 7, 'rna3p_pur': 33, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 74} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 0 Ad-hoc single atom residues: {' CA': 28} Chain breaks: 28 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.83, per 1000 atoms: 0.24 Number of scatterers: 12015 At special positions: 0 Unit cell: (128.563, 146.189, 172.109, 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 29 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: 0.89 Conformation dependent library (CDL) restraints added in 215.3 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 48.3% alpha, 16.4% beta 174 base pairs and 310 stacking pairs defined. Time for finding SS restraints: 1.96 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 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: 7.369A 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: 7.237A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 440 hydrogen bonds 746 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 310 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.27 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: 1148 1.33 - 1.44: 6363 1.44 - 1.56: 4773 1.56 - 1.68: 1026 1.68 - 1.80: 5 Bond restraints: 13315 Sorted by residual: 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 1.13e+01 bond pdb=" N LEU B 111 " pdb=" CA LEU B 111 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.32e+00 bond pdb=" P A A 50 " pdb=" O5' A A 50 " ideal model delta sigma weight residual 1.593 1.551 0.042 1.50e-02 4.44e+03 7.90e+00 bond pdb=" N VAL B 97 " pdb=" CA VAL B 97 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.62e+00 bond pdb=" N GLY B 93 " pdb=" CA GLY B 93 " ideal model delta sigma weight residual 1.450 1.478 -0.028 1.04e-02 9.25e+03 7.05e+00 ... (remaining 13310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18508 2.33 - 4.66: 1382 4.66 - 7.00: 606 7.00 - 9.33: 44 9.33 - 11.66: 6 Bond angle restraints: 20546 Sorted by residual: angle pdb=" C4' G A 236 " pdb=" C3' G A 236 " pdb=" C2' G A 236 " ideal model delta sigma weight residual 102.60 96.78 5.82 1.00e+00 1.00e+00 3.39e+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 96.92 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" O3' C C 69 " pdb=" P G C 70 " pdb=" O5' G C 70 " ideal model delta sigma weight residual 104.00 95.57 8.43 1.50e+00 4.44e-01 3.16e+01 angle pdb=" O3' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " ideal model delta sigma weight residual 109.50 117.84 -8.34 1.50e+00 4.44e-01 3.09e+01 angle pdb=" O3' C A 176 " pdb=" C3' C A 176 " pdb=" C2' C A 176 " ideal model delta sigma weight residual 113.70 121.63 -7.93 1.50e+00 4.44e-01 2.79e+01 ... (remaining 20541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 7065 35.94 - 71.88: 1423 71.88 - 107.82: 174 107.82 - 143.76: 6 143.76 - 179.70: 8 Dihedral angle restraints: 8676 sinusoidal: 8339 harmonic: 337 Sorted by residual: 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 16.23 -176.23 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U C 59 " pdb=" C1' U C 59 " pdb=" N1 U C 59 " pdb=" C2 U C 59 " ideal model delta sinusoidal sigma weight residual 232.00 52.34 179.66 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 232.00 58.55 173.45 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 8673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1967 0.112 - 0.224: 415 0.224 - 0.336: 61 0.336 - 0.448: 187 0.448 - 0.560: 81 Chirality restraints: 2711 Sorted by residual: 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 7.84e+00 chirality pdb=" P C C 47 " pdb=" OP1 C C 47 " pdb=" OP2 C C 47 " pdb=" O5' C C 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" P G E -13 " pdb=" OP1 G E -13 " pdb=" OP2 G E -13 " pdb=" O5' G E -13 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.59e+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 " -0.004 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 2.05e-02 1.26e+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 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 299 " 0.008 2.00e-02 2.50e+03 pdb=" C2 G A 299 " -0.002 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' A A 187 " 0.038 2.00e-02 2.50e+03 1.64e-02 7.42e+00 pdb=" N9 A A 187 " -0.033 2.00e-02 2.50e+03 pdb=" C8 A A 187 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A A 187 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A A 187 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 187 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A A 187 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A A 187 " 0.009 2.00e-02 2.50e+03 pdb=" C2 A A 187 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A A 187 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A A 187 " -0.006 2.00e-02 2.50e+03 ... (remaining 676 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 4 1.81 - 2.58: 171 2.58 - 3.36: 14360 3.36 - 4.13: 46478 4.13 - 4.90: 56847 Nonbonded interactions: 117860 Sorted by model distance: nonbonded pdb=" OP2 U A 293 " pdb="CA CA A 523 " model vdw 1.038 3.250 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 1.368 3.690 nonbonded pdb=" OP2 A A 364 " pdb=" N9 G A 365 " model vdw 1.835 3.120 ... (remaining 117855 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: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 13.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 0.044 13315 Z= 0.622 Angle : 1.510 11.659 20546 Z= 0.901 Chirality : 0.158 0.560 2711 Planarity : 0.008 0.186 679 Dihedral : 27.542 179.700 8460 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 26.26 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.81), residues: 114 helix: 1.98 (0.83), residues: 46 sheet: 0.87 (0.82), residues: 29 loop : -0.02 (1.09), 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 0.00868 / 0.62 (13315) covalent geometry : angle 1.51012 / 0.90 (20546) hydrogen bonds : bond 0.18189 / 18.92 ( 487) hydrogen bonds : angle 8.99017 / 10.82 ( 875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8179 (mp0) REVERT: B 46 SER cc_start: 0.9299 (m) cc_final: 0.8974 (p) outliers start: 5 outliers final: 1 residues processed: 24 average time/residue: 0.6395 time to fit residues: 16.6594 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.085648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.051480 restraints weight = 47883.685| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.93 r_work: 0.2979 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 13315 Z= 0.499 Angle : 0.754 10.373 20546 Z= 0.448 Chirality : 0.054 0.438 2711 Planarity : 0.007 0.035 679 Dihedral : 26.879 179.393 8207 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % 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: 1.17 (0.82), residues: 114 helix: 1.56 (0.77), residues: 53 sheet: 0.50 (0.82), residues: 29 loop : -0.14 (1.28), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.011 0.002 TYR B 94 PHE 0.010 0.003 PHE B 68 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.50 (13315) covalent geometry : angle 0.75402 / 0.45 (20546) hydrogen bonds : bond 0.12089 / 12.47 ( 487) hydrogen bonds : angle 2.77535 / 3.10 ( 875) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8287 (mp0) REVERT: B 12 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8625 (mt-10) REVERT: B 46 SER cc_start: 0.9378 (m) cc_final: 0.8978 (p) REVERT: B 92 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8734 (mtp) outliers start: 9 outliers final: 4 residues processed: 26 average time/residue: 0.7011 time to fit residues: 19.5164 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL 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 23 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.086319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.052852 restraints weight = 48314.159| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.11 r_work: 0.3002 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13315 Z= 0.287 Angle : 0.554 8.292 20546 Z= 0.347 Chirality : 0.040 0.334 2711 Planarity : 0.005 0.027 679 Dihedral : 26.713 176.182 8207 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 8.08 % Allowed : 28.28 % 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: 1.29 (0.83), residues: 114 helix: 2.09 (0.79), residues: 47 sheet: 0.32 (0.78), residues: 29 loop : -0.20 (1.24), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.007 0.002 TYR B 5 PHE 0.010 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.29 (13315) covalent geometry : angle 0.55414 / 0.35 (20546) hydrogen bonds : bond 0.09043 / 9.46 ( 487) hydrogen bonds : angle 2.56189 / 2.94 ( 875) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8181 (mp0) REVERT: B 12 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8619 (mt-10) REVERT: B 46 SER cc_start: 0.9406 (m) cc_final: 0.8951 (p) REVERT: B 92 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8790 (mtp) outliers start: 8 outliers final: 5 residues processed: 26 average time/residue: 0.7563 time to fit residues: 21.0477 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 : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 105 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 0 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 40.0000 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.085421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.051482 restraints weight = 48256.018| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.65 r_work: 0.2953 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13315 Z= 0.413 Angle : 0.635 9.410 20546 Z= 0.388 Chirality : 0.046 0.416 2711 Planarity : 0.006 0.036 679 Dihedral : 26.547 179.011 8207 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 7.07 % Allowed : 29.29 % 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: 0.65 (0.79), residues: 114 helix: 1.46 (0.74), residues: 47 sheet: 0.02 (0.77), residues: 29 loop : -0.40 (1.21), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 59 TYR 0.011 0.002 TYR B 94 PHE 0.010 0.002 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.41 (13315) covalent geometry : angle 0.63539 / 0.39 (20546) hydrogen bonds : bond 0.10437 / 10.62 ( 487) hydrogen bonds : angle 2.61548 / 2.96 ( 875) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8162 (pm20) REVERT: B 12 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8642 (mt-10) REVERT: B 46 SER cc_start: 0.9402 (m) cc_final: 0.8913 (p) outliers start: 7 outliers final: 3 residues processed: 25 average time/residue: 0.6554 time to fit residues: 17.6947 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 : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.085992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.052487 restraints weight = 48112.242| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.21 r_work: 0.2987 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13315 Z= 0.308 Angle : 0.548 9.799 20546 Z= 0.341 Chirality : 0.040 0.352 2711 Planarity : 0.005 0.024 679 Dihedral : 26.480 175.303 8207 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 9.09 % Allowed : 26.26 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.82), residues: 114 helix: 1.71 (0.77), residues: 47 sheet: -0.63 (0.76), residues: 31 loop : -0.15 (1.27), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.006 0.001 TYR B 31 PHE 0.011 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.31 (13315) covalent geometry : angle 0.54776 / 0.34 (20546) hydrogen bonds : bond 0.08436 / 8.70 ( 487) hydrogen bonds : angle 2.42565 / 2.79 ( 875) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8154 (pm20) REVERT: B 12 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: B 46 SER cc_start: 0.9390 (m) cc_final: 0.8934 (p) outliers start: 9 outliers final: 4 residues processed: 27 average time/residue: 0.6644 time to fit residues: 19.3431 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 50.0000 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.085752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052004 restraints weight = 47740.586| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.36 r_work: 0.3000 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13315 Z= 0.325 Angle : 0.563 9.999 20546 Z= 0.349 Chirality : 0.040 0.376 2711 Planarity : 0.005 0.029 679 Dihedral : 26.414 176.009 8207 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 6.06 % Allowed : 30.30 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.82), residues: 114 helix: 1.67 (0.78), residues: 47 sheet: -0.17 (0.75), residues: 29 loop : -0.44 (1.25), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.006 0.001 TYR B 5 PHE 0.010 0.002 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.32 (13315) covalent geometry : angle 0.56262 / 0.35 (20546) hydrogen bonds : bond 0.08938 / 9.12 ( 487) hydrogen bonds : angle 2.44063 / 2.83 ( 875) *********************** 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 : 0.156 Fit side-chains REVERT: B 11 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8134 (pm20) REVERT: B 12 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8656 (mt-10) REVERT: B 18 GLN cc_start: 0.8928 (mt0) cc_final: 0.8532 (mp10) REVERT: B 46 SER cc_start: 0.9389 (m) cc_final: 0.8936 (p) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 0.7094 time to fit residues: 18.3210 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 50.0000 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.086965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.052663 restraints weight = 48533.593| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.16 r_work: 0.3015 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2771 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= 0.282 Angle : 0.524 9.989 20546 Z= 0.327 Chirality : 0.039 0.339 2711 Planarity : 0.005 0.025 679 Dihedral : 26.388 175.272 8207 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 7.07 % Allowed : 28.28 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.82), residues: 114 helix: 1.72 (0.78), residues: 47 sheet: -0.56 (0.76), residues: 31 loop : -0.12 (1.24), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.010 0.001 TYR B 94 PHE 0.009 0.002 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.28 (13315) covalent geometry : angle 0.52380 / 0.33 (20546) hydrogen bonds : bond 0.08029 / 8.27 ( 487) hydrogen bonds : angle 2.35993 / 2.75 ( 875) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8124 (pm20) REVERT: B 12 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: B 46 SER cc_start: 0.9365 (m) cc_final: 0.8945 (p) outliers start: 7 outliers final: 4 residues processed: 24 average time/residue: 0.6694 time to fit residues: 17.3095 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 40.0000 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.085112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.051015 restraints weight = 47418.038| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.72 r_work: 0.2968 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13315 Z= 0.445 Angle : 0.634 9.332 20546 Z= 0.386 Chirality : 0.047 0.432 2711 Planarity : 0.006 0.035 679 Dihedral : 26.384 176.811 8207 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.05 % Allowed : 32.32 % 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: 0.52 (0.80), residues: 114 helix: 1.38 (0.78), residues: 46 sheet: -0.19 (0.77), residues: 29 loop : -0.34 (1.17), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.006 0.002 TYR B 31 PHE 0.008 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.44 (13315) covalent geometry : angle 0.63392 / 0.39 (20546) hydrogen bonds : bond 0.10312 / 10.37 ( 487) hydrogen bonds : angle 2.51252 / 2.93 ( 875) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8066 (pm20) REVERT: B 12 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: B 46 SER cc_start: 0.9381 (m) cc_final: 0.8930 (p) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.7294 time to fit residues: 17.2100 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 : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.085853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.052829 restraints weight = 47421.350| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.15 r_work: 0.3007 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13315 Z= 0.296 Angle : 0.536 8.416 20546 Z= 0.335 Chirality : 0.039 0.355 2711 Planarity : 0.005 0.022 679 Dihedral : 26.391 175.179 8207 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.03 % Allowed : 34.34 % 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: 0.67 (0.83), residues: 114 helix: 1.68 (0.80), residues: 47 sheet: -0.63 (0.77), residues: 31 loop : -0.01 (1.24), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.006 0.001 TYR B 31 PHE 0.010 0.002 PHE B 28 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.30 (13315) covalent geometry : angle 0.53550 / 0.33 (20546) hydrogen bonds : bond 0.08303 / 8.44 ( 487) hydrogen bonds : angle 2.36755 / 2.77 ( 875) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.157 Fit side-chains REVERT: B 11 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8168 (pm20) REVERT: B 12 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8619 (mt-10) REVERT: B 18 GLN cc_start: 0.8935 (mt0) cc_final: 0.8547 (mp10) REVERT: B 46 SER cc_start: 0.9367 (m) cc_final: 0.8961 (p) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.7352 time to fit residues: 17.3501 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.086772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.052779 restraints weight = 48721.295| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.16 r_work: 0.3006 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13315 Z= 0.278 Angle : 0.525 9.162 20546 Z= 0.329 Chirality : 0.039 0.347 2711 Planarity : 0.005 0.027 679 Dihedral : 26.374 175.127 8207 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.03 % Allowed : 34.34 % 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: 0.69 (0.83), residues: 114 helix: 1.65 (0.80), residues: 47 sheet: -0.58 (0.77), residues: 31 loop : 0.01 (1.27), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.007 0.002 TYR B 5 PHE 0.009 0.002 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.28 (13315) covalent geometry : angle 0.52523 / 0.33 (20546) hydrogen bonds : bond 0.08317 / 8.42 ( 487) hydrogen bonds : angle 2.38249 / 2.80 ( 875) ********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8174 (pm20) REVERT: B 12 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8628 (mt-10) REVERT: B 46 SER cc_start: 0.9360 (m) cc_final: 0.8962 (p) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.7465 time to fit residues: 17.5469 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.086252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.051643 restraints weight = 48446.627| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.60 r_work: 0.2976 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13315 Z= 0.392 Angle : 0.602 8.990 20546 Z= 0.369 Chirality : 0.044 0.421 2711 Planarity : 0.006 0.034 679 Dihedral : 26.348 175.348 8207 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 0.56 (0.81), residues: 114 helix: 1.43 (0.77), residues: 47 sheet: -0.11 (0.78), residues: 29 loop : -0.44 (1.22), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.007 0.002 TYR B 5 PHE 0.009 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.39 (13315) covalent geometry : angle 0.60150 / 0.37 (20546) hydrogen bonds : bond 0.09631 / 9.65 ( 487) hydrogen bonds : angle 2.46478 / 2.87 ( 875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5823.99 seconds wall clock time: 99 minutes 26.29 seconds (5966.29 seconds total)