Starting phenix.real_space_refine on Fri Jul 3 02:00:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owv_70945/07_2026/9owv_70945_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owv_70945/07_2026/9owv_70945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9owv_70945/07_2026/9owv_70945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owv_70945/07_2026/9owv_70945.map" model { file = "/net/cci-nas-00/data/ceres_data/9owv_70945/07_2026/9owv_70945_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owv_70945/07_2026/9owv_70945_neut.cif" } resolution = 3.02 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= 0.008 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 27 9.91 5 P 492 5.49 5 S 3 5.16 5 C 5317 2.51 5 N 2119 2.21 5 O 3579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 11537 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': 27, 'rna2p_pyr': 14, 'rna3p_pur': 216, 'rna3p_pyr': 160} Link IDs: {'rna2p': 41, 'rna3p': 375} Chain: "C" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1601 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 62} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 0 Ad-hoc single atom residues: {' CA': 24} Chain breaks: 24 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 2.09, per 1000 atoms: 0.18 Number of scatterers: 11537 At special positions: 0 Unit cell: (125.453, 146.189, 173.146, 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 27 19.99 S 3 16.00 P 492 15.00 O 3579 8.00 N 2119 7.00 C 5317 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: 0.87 Conformation dependent library (CDL) restraints added in 74.8 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 49.1% alpha, 16.4% beta 163 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 2.42 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 93 through 108 removed outlier: 3.707A 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: 6.091A 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: 6.191A 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) 48 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 413 hydrogen bonds 704 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1067 1.32 - 1.44: 6119 1.44 - 1.56: 4614 1.56 - 1.68: 983 1.68 - 1.80: 5 Bond restraints: 12788 Sorted by residual: bond pdb=" CA SER B 100 " pdb=" CB SER B 100 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.23e+01 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.353 0.021 6.00e-03 2.78e+04 1.18e+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 9.21e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.25e-02 6.40e+03 9.13e+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 7.67e+00 ... (remaining 12783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 17698 2.53 - 5.05: 1443 5.05 - 7.58: 554 7.58 - 10.10: 29 10.10 - 12.63: 6 Bond angle restraints: 19730 Sorted by residual: angle pdb=" O3' A A 240 " pdb=" C3' A A 240 " pdb=" C2' A A 240 " ideal model delta sigma weight residual 113.70 103.13 10.57 1.50e+00 4.44e-01 4.97e+01 angle pdb=" O3' G C 63 " pdb=" P U C 64 " pdb=" O5' U C 64 " ideal model delta sigma weight residual 104.00 93.68 10.32 1.50e+00 4.44e-01 4.73e+01 angle pdb=" O3' A A 49 " pdb=" P A A 50 " pdb=" O5' A A 50 " ideal model delta sigma weight residual 104.00 94.33 9.67 1.50e+00 4.44e-01 4.16e+01 angle pdb=" O3' G A 108 " pdb=" P C A 109 " pdb=" O5' C A 109 " ideal model delta sigma weight residual 104.00 95.07 8.93 1.50e+00 4.44e-01 3.55e+01 angle pdb=" O2' C A 258 " pdb=" C2' C A 258 " pdb=" C1' C A 258 " ideal model delta sigma weight residual 108.40 99.98 8.42 1.50e+00 4.44e-01 3.15e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 6736 35.64 - 71.27: 1378 71.27 - 106.91: 184 106.91 - 142.54: 7 142.54 - 178.18: 6 Dihedral angle restraints: 8311 sinusoidal: 7974 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 200.00 21.82 178.18 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" CD ARG B 86 " pdb=" NE ARG B 86 " pdb=" CZ ARG B 86 " pdb=" NH1 ARG B 86 " ideal model delta sinusoidal sigma weight residual 0.00 -76.29 76.29 1 1.00e+01 1.00e-02 7.33e+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 61.50 170.50 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 8308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1828 0.118 - 0.235: 428 0.235 - 0.353: 64 0.353 - 0.471: 239 0.471 - 0.589: 37 Chirality restraints: 2596 Sorted by residual: chirality pdb=" P G A 136 " pdb=" OP1 G A 136 " pdb=" OP2 G A 136 " pdb=" O5' G A 136 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.66e+00 chirality pdb=" P G A 268 " pdb=" OP1 G A 268 " pdb=" OP2 G A 268 " pdb=" O5' G A 268 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.32e+00 chirality pdb=" P C A 123 " pdb=" OP1 C A 123 " pdb=" OP2 C A 123 " pdb=" O5' C A 123 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 2593 not shown) Planarity restraints: 656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 86 " -1.072 9.50e-02 1.11e+02 4.80e-01 1.39e+02 pdb=" NE ARG B 86 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 86 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 86 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 86 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 26 " 0.969 9.50e-02 1.11e+02 4.34e-01 1.14e+02 pdb=" NE ARG B 26 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 26 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 26 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 26 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " -0.415 9.50e-02 1.11e+02 1.86e-01 2.12e+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 ... (remaining 653 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 12 2.05 - 2.76: 2442 2.76 - 3.47: 15989 3.47 - 4.19: 43809 4.19 - 4.90: 51031 Nonbonded interactions: 113283 Sorted by model distance: 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 1.362 3.260 nonbonded pdb=" C3' A A 363 " pdb=" C8 A A 364 " model vdw 1.368 3.690 nonbonded pdb=" OP1 G C 1 " pdb="CA CA C 101 " model vdw 1.508 3.250 nonbonded pdb=" OP2 A A 50 " pdb="CA CA C 101 " model vdw 1.567 3.250 ... (remaining 113278 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: 4.560 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 0.054 12788 Z= 0.639 Angle : 1.613 12.629 19730 Z= 0.951 Chirality : 0.167 0.589 2596 Planarity : 0.027 0.480 656 Dihedral : 27.739 178.179 8095 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 14.14 % Allowed : 21.21 % 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: 0.33 (0.83), residues: 114 helix: 0.90 (0.82), residues: 46 sheet: 0.82 (0.83), residues: 29 loop : -1.01 (1.16), 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 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.64 (12788) covalent geometry : angle 1.61313 / 0.95 (19730) hydrogen bonds : bond 0.19048 / 18.16 ( 461) hydrogen bonds : angle 11.21471 / 13.13 ( 833) *********************** 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 47 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6695 (mmtm) outliers start: 14 outliers final: 7 residues processed: 41 average time/residue: 0.1430 time to fit residues: 7.8835 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.075117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048571 restraints weight = 61588.439| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.67 r_work: 0.3114 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12788 Z= 0.312 Angle : 0.686 7.075 19730 Z= 0.421 Chirality : 0.045 0.291 2596 Planarity : 0.006 0.042 656 Dihedral : 26.959 176.019 7862 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 12.12 % Allowed : 21.21 % 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: 0.68 (0.79), residues: 114 helix: 0.54 (0.75), residues: 46 sheet: 1.19 (0.87), residues: 29 loop : -0.05 (1.13), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.007 0.002 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 0.00480 / 0.31 (12788) covalent geometry : angle 0.68639 / 0.42 (19730) hydrogen bonds : bond 0.11660 / 12.34 ( 461) hydrogen bonds : angle 2.99106 / 3.30 ( 833) *********************** 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 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6195 (mmtm) REVERT: B 12 GLU cc_start: 0.8270 (mp0) cc_final: 0.7973 (mp0) outliers start: 12 outliers final: 6 residues processed: 31 average time/residue: 0.1373 time to fit residues: 5.9063 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 : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 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 = 0.3956 r_free = 0.3956 target = 0.072891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.046203 restraints weight = 60704.046| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.27 r_work: 0.2918 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 12788 Z= 0.361 Angle : 0.661 11.080 19730 Z= 0.401 Chirality : 0.043 0.263 2596 Planarity : 0.007 0.076 656 Dihedral : 26.734 175.675 7847 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: 0.72 (0.85), residues: 114 helix: 0.67 (0.78), residues: 46 sheet: 1.15 (0.89), residues: 29 loop : -0.12 (1.29), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG B 35 TYR 0.023 0.003 TYR B 31 PHE 0.020 0.003 PHE B 41 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.36 (12788) covalent geometry : angle 0.66150 / 0.40 (19730) hydrogen bonds : bond 0.10628 / 10.56 ( 461) hydrogen bonds : angle 2.91680 / 3.13 ( 833) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.6007 (mmtm) REVERT: B 12 GLU cc_start: 0.8316 (mp0) cc_final: 0.7974 (pm20) REVERT: B 27 GLN cc_start: 0.8862 (mp10) cc_final: 0.8516 (mp10) outliers start: 9 outliers final: 7 residues processed: 26 average time/residue: 0.1259 time to fit residues: 4.6064 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS 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 75 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.071574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043963 restraints weight = 61655.005| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.40 r_work: 0.2885 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 12788 Z= 0.508 Angle : 0.752 10.086 19730 Z= 0.452 Chirality : 0.051 0.278 2596 Planarity : 0.007 0.027 656 Dihedral : 26.680 176.256 7847 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 9.09 % Allowed : 25.25 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.84), residues: 114 helix: 0.28 (0.75), residues: 46 sheet: 0.76 (0.95), residues: 29 loop : -0.56 (1.24), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.015 0.003 TYR B 40 PHE 0.017 0.004 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.51 (12788) covalent geometry : angle 0.75165 / 0.45 (19730) hydrogen bonds : bond 0.11485 / 11.25 ( 461) hydrogen bonds : angle 2.99783 / 3.25 ( 833) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6064 (mmtt) REVERT: B 27 GLN cc_start: 0.8985 (mp10) cc_final: 0.8605 (mp10) REVERT: B 29 VAL cc_start: 0.8082 (t) cc_final: 0.7534 (p) REVERT: B 41 PHE cc_start: 0.8784 (p90) cc_final: 0.8573 (p90) outliers start: 9 outliers final: 5 residues processed: 29 average time/residue: 0.1139 time to fit residues: 4.6203 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.070951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.045674 restraints weight = 61828.653| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.14 r_work: 0.2824 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 12788 Z= 0.608 Angle : 0.818 9.559 19730 Z= 0.486 Chirality : 0.056 0.291 2596 Planarity : 0.007 0.032 656 Dihedral : 26.816 177.892 7847 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.07 % Allowed : 24.24 % 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: -0.59 (0.80), residues: 114 helix: 0.07 (0.74), residues: 47 sheet: -0.82 (0.92), residues: 31 loop : -0.26 (1.17), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 86 TYR 0.018 0.003 TYR B 40 PHE 0.029 0.005 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00925 / 0.61 (12788) covalent geometry : angle 0.81762 / 0.49 (19730) hydrogen bonds : bond 0.13023 / 13.00 ( 461) hydrogen bonds : angle 3.09088 / 3.54 ( 833) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5649 (mmtm) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.1258 time to fit residues: 4.6660 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 : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 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 = 0.3920 r_free = 0.3920 target = 0.072198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.044569 restraints weight = 59442.966| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.08 r_work: 0.2892 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12788 Z= 0.416 Angle : 0.640 9.393 19730 Z= 0.397 Chirality : 0.046 0.248 2596 Planarity : 0.006 0.025 656 Dihedral : 26.763 175.125 7847 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.07 % Allowed : 24.24 % 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: 0.19 (0.79), residues: 114 helix: 0.32 (0.75), residues: 47 sheet: 0.65 (0.95), residues: 29 loop : -0.35 (1.06), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.006 0.002 TYR B 40 PHE 0.012 0.002 PHE B 28 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.42 (12788) covalent geometry : angle 0.63993 / 0.40 (19730) hydrogen bonds : bond 0.09725 / 9.80 ( 461) hydrogen bonds : angle 2.79072 / 3.12 ( 833) *********************** 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: 7 poor density : 20 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5802 (mmtm) REVERT: B 5 TYR cc_start: 0.8296 (m-80) cc_final: 0.7864 (m-80) REVERT: B 12 GLU cc_start: 0.8063 (pm20) cc_final: 0.7721 (pm20) REVERT: B 71 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8057 (pp) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 0.1288 time to fit residues: 4.8183 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 : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.071626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.043925 restraints weight = 59790.010| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.53 r_work: 0.2863 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 12788 Z= 0.556 Angle : 0.755 8.571 19730 Z= 0.456 Chirality : 0.054 0.268 2596 Planarity : 0.007 0.028 656 Dihedral : 26.715 179.357 7847 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.07 % Allowed : 23.23 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.78), residues: 114 helix: 0.12 (0.73), residues: 47 sheet: 0.63 (1.03), residues: 26 loop : -0.04 (1.00), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 6 TYR 0.007 0.002 TYR B 94 PHE 0.010 0.002 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.56 (12788) covalent geometry : angle 0.75533 / 0.46 (19730) hydrogen bonds : bond 0.12199 / 12.25 ( 461) hydrogen bonds : angle 2.89985 / 3.27 ( 833) *********************** 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 : 0.187 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5812 (mmtm) REVERT: B 5 TYR cc_start: 0.8396 (m-80) cc_final: 0.7953 (m-80) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 0.1221 time to fit residues: 4.5346 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 : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.071699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.044847 restraints weight = 60329.924| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.22 r_work: 0.2966 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 12788 Z= 0.508 Angle : 0.717 7.262 19730 Z= 0.434 Chirality : 0.051 0.286 2596 Planarity : 0.006 0.030 656 Dihedral : 26.730 177.227 7845 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 8.08 % Allowed : 22.22 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.75), residues: 114 helix: 0.03 (0.72), residues: 47 sheet: 0.16 (0.87), residues: 29 loop : -0.36 (1.02), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.010 0.002 TYR B 40 PHE 0.017 0.003 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.51 (12788) covalent geometry : angle 0.71680 / 0.43 (19730) hydrogen bonds : bond 0.10317 / 10.45 ( 461) hydrogen bonds : angle 2.86890 / 3.34 ( 833) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5808 (mmtm) REVERT: B 5 TYR cc_start: 0.8441 (m-80) cc_final: 0.8020 (m-80) REVERT: B 12 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7877 (pm20) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 0.1216 time to fit residues: 4.7027 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 40.0000 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.071699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044851 restraints weight = 59479.735| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.20 r_work: 0.2957 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12788 Z= 0.468 Angle : 0.693 8.832 19730 Z= 0.423 Chirality : 0.049 0.281 2596 Planarity : 0.006 0.033 656 Dihedral : 26.692 179.757 7845 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.67 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: 0.03 (0.78), residues: 114 helix: 0.23 (0.76), residues: 46 sheet: 0.12 (0.99), residues: 28 loop : -0.04 (0.98), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 6 TYR 0.006 0.002 TYR B 40 PHE 0.006 0.002 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.47 (12788) covalent geometry : angle 0.69292 / 0.42 (19730) hydrogen bonds : bond 0.10961 / 11.09 ( 461) hydrogen bonds : angle 2.81429 / 3.23 ( 833) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5843 (mmtm) REVERT: B 5 TYR cc_start: 0.8418 (m-80) cc_final: 0.8016 (m-80) REVERT: B 96 GLU cc_start: 0.8685 (pm20) cc_final: 0.8333 (pm20) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.1369 time to fit residues: 4.8511 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 : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 40.0000 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.071322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.044267 restraints weight = 61529.803| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.85 r_work: 0.2976 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12788 Z= 0.317 Angle : 0.597 8.400 19730 Z= 0.371 Chirality : 0.042 0.271 2596 Planarity : 0.006 0.034 656 Dihedral : 26.650 176.459 7845 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.05 % Allowed : 25.25 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.79), residues: 114 helix: 0.40 (0.78), residues: 46 sheet: 1.10 (1.02), residues: 26 loop : -0.23 (0.95), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 6 TYR 0.008 0.001 TYR B 40 PHE 0.007 0.002 PHE B 13 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.32 (12788) covalent geometry : angle 0.59678 / 0.37 (19730) hydrogen bonds : bond 0.08915 / 9.12 ( 461) hydrogen bonds : angle 2.72641 / 3.20 ( 833) ********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.5892 (mmtm) REVERT: B 5 TYR cc_start: 0.8472 (m-80) cc_final: 0.8100 (m-80) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.1369 time to fit residues: 4.7850 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 : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 50.0000 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 40.0000 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 6.6390 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.070430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.044182 restraints weight = 61794.703| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.04 r_work: 0.2881 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 12788 Z= 0.575 Angle : 0.780 9.813 19730 Z= 0.465 Chirality : 0.054 0.301 2596 Planarity : 0.007 0.034 656 Dihedral : 26.621 179.859 7845 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.05 % Allowed : 24.24 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.79), residues: 114 helix: 0.18 (0.78), residues: 46 sheet: 0.35 (0.99), residues: 28 loop : -0.00 (1.00), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 6 TYR 0.009 0.002 TYR B 40 PHE 0.007 0.002 PHE B 41 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00869 / 0.57 (12788) covalent geometry : angle 0.77978 / 0.46 (19730) hydrogen bonds : bond 0.11946 / 11.94 ( 461) hydrogen bonds : angle 2.89763 / 3.40 ( 833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4073.93 seconds wall clock time: 70 minutes 21.46 seconds (4221.46 seconds total)