Starting phenix.real_space_refine on Wed Aug 5 19:54:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owv_70945/08_2026/9owv_70945_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owv_70945/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9owv_70945/08_2026/9owv_70945_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owv_70945/08_2026/9owv_70945_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9owv_70945/08_2026/9owv_70945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owv_70945/08_2026/9owv_70945.map" } 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-2.2rc3-6140/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, 24 Unusual residues: {' CA': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.16, per 1000 atoms: 0.19 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: 0.65 Conformation dependent library (CDL) restraints added in 68.1 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: 2.13 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: 2.72 Time building geometry restraints manager: 0.91 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=" P C A 123 " pdb=" O5' C A 123 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 7.92e+00 ... (remaining 12783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 17726 2.53 - 5.05: 1408 5.05 - 7.58: 561 7.58 - 10.10: 28 10.10 - 12.63: 7 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 1.60e+00 3.91e-01 4.37e+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 1.90e+00 2.77e-01 2.95e+01 angle pdb=" C3' U C 46 " pdb=" O3' U C 46 " pdb=" P C C 47 " ideal model delta sigma weight residual 119.70 125.83 -6.13 1.20e+00 6.94e-01 2.61e+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 1.90e+00 2.77e-01 2.59e+01 angle pdb=" C3' C A 159 " pdb=" C2' C A 159 " pdb=" C1' C A 159 " ideal model delta sigma weight residual 101.30 104.80 -3.50 7.00e-01 2.04e+00 2.50e+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: 1775 0.118 - 0.235: 481 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 2.510 nonbonded pdb=" OP2 A A 50 " pdb="CA CA C 101 " model vdw 1.567 2.510 ... (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: 5.510 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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= 0.699 Angle : 1.612 12.629 19730 Z= 0.958 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 0.00922 / 0.70 (12788) covalent geometry : angle 1.61218 / 0.96 (19730) hydrogen bonds : bond 0.19048 / 20.36 ( 461) hydrogen bonds : angle 11.21471 / 13.72 ( 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 : 0.136 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6670 (mmtt) outliers start: 14 outliers final: 7 residues processed: 41 average time/residue: 0.1340 time to fit residues: 7.2786 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 : 0.120 ------------------------------------------------------------------------------- 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: 0.6980 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.075871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.047226 restraints weight = 59846.290| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.36 r_work: 0.3079 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12788 Z= 0.328 Angle : 0.847 10.610 19730 Z= 0.453 Chirality : 0.058 0.376 2596 Planarity : 0.007 0.041 656 Dihedral : 26.830 175.687 7862 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 10.10 % Allowed : 23.23 % 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: 0.73 (0.78), residues: 114 helix: 0.64 (0.73), residues: 46 sheet: 1.17 (0.86), residues: 29 loop : -0.06 (1.14), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.007 0.002 TYR B 31 PHE 0.012 0.003 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.33 (12788) covalent geometry : angle 0.84664 / 0.45 (19730) hydrogen bonds : bond 0.12006 / 13.56 ( 461) hydrogen bonds : angle 2.98963 / 3.52 ( 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6167 (mmtm) REVERT: B 12 GLU cc_start: 0.8209 (mp0) cc_final: 0.7948 (mp0) outliers start: 10 outliers final: 7 residues processed: 31 average time/residue: 0.1103 time to fit residues: 4.7922 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 : 0.118 ------------------------------------------------------------------------------- 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 53 LYS 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: 6.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.073326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.046215 restraints weight = 60925.081| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.23 r_work: 0.3022 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 12788 Z= 0.331 Angle : 0.752 9.980 19730 Z= 0.409 Chirality : 0.050 0.385 2596 Planarity : 0.007 0.063 656 Dihedral : 26.614 174.686 7851 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 11.11 % Allowed : 24.24 % 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: 0.72 (0.83), residues: 114 helix: 0.73 (0.78), residues: 46 sheet: 1.15 (0.90), residues: 29 loop : -0.19 (1.19), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 26 TYR 0.012 0.003 TYR B 31 PHE 0.014 0.002 PHE B 41 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.33 (12788) covalent geometry : angle 0.75195 / 0.41 (19730) hydrogen bonds : bond 0.10639 / 11.72 ( 461) hydrogen bonds : angle 2.91166 / 3.39 ( 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6224 (mmtm) REVERT: B 12 GLU cc_start: 0.8335 (mp0) cc_final: 0.8049 (pm20) REVERT: B 27 GLN cc_start: 0.8915 (mp10) cc_final: 0.8516 (mp10) outliers start: 11 outliers final: 8 residues processed: 29 average time/residue: 0.1041 time to fit residues: 4.2670 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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 53 LYS 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: 0.3980 chunk 12 optimal weight: 40.0000 chunk 43 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 7.0788 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.071145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.043148 restraints weight = 61768.032| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.19 r_work: 0.2858 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 12788 Z= 0.585 Angle : 1.107 11.218 19730 Z= 0.550 Chirality : 0.075 0.410 2596 Planarity : 0.008 0.050 656 Dihedral : 26.647 179.569 7851 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 10.10 % Allowed : 26.26 % 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: -0.21 (0.82), residues: 114 helix: 0.07 (0.75), residues: 46 sheet: 0.61 (0.94), residues: 29 loop : -0.81 (1.18), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 106 TYR 0.024 0.003 TYR B 40 PHE 0.010 0.003 PHE B 41 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.58 (12788) covalent geometry : angle 1.10683 / 0.55 (19730) hydrogen bonds : bond 0.13442 / 14.83 ( 461) hydrogen bonds : angle 3.11013 / 3.76 ( 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 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6047 (mmtm) REVERT: B 27 GLN cc_start: 0.8894 (mp10) cc_final: 0.8486 (mp10) outliers start: 10 outliers final: 6 residues processed: 32 average time/residue: 0.1077 time to fit residues: 4.7299 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 : 0.159 ------------------------------------------------------------------------------- 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 53 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: 10.0000 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.071685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043995 restraints weight = 60041.518| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.00 r_work: 0.2856 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 12788 Z= 0.607 Angle : 1.129 12.271 19730 Z= 0.547 Chirality : 0.074 0.383 2596 Planarity : 0.008 0.047 656 Dihedral : 26.817 178.458 7851 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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: -0.54 (0.81), residues: 114 helix: -0.22 (0.72), residues: 47 sheet: -0.63 (0.94), residues: 31 loop : 0.14 (1.23), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 86 TYR 0.017 0.004 TYR B 40 PHE 0.018 0.006 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.61 (12788) covalent geometry : angle 1.12949 / 0.55 (19730) hydrogen bonds : bond 0.13258 / 14.88 ( 461) hydrogen bonds : angle 3.15305 / 3.82 ( 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5791 (mmtm) REVERT: B 5 TYR cc_start: 0.8352 (m-80) cc_final: 0.7953 (m-80) REVERT: B 71 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (pp) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.1129 time to fit residues: 3.8955 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 : 0.127 ------------------------------------------------------------------------------- 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 53 LYS Chi-restraints excluded: chain B residue 71 LEU 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: 5.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 36 optimal weight: 50.0000 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.071849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.044279 restraints weight = 58589.544| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.46 r_work: 0.2883 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12788 Z= 0.383 Angle : 0.839 8.733 19730 Z= 0.437 Chirality : 0.057 0.374 2596 Planarity : 0.006 0.033 656 Dihedral : 26.643 176.797 7851 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.06 (0.79), residues: 114 helix: 0.20 (0.75), residues: 47 sheet: 0.29 (0.94), residues: 29 loop : -0.07 (1.11), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 86 TYR 0.005 0.001 TYR B 5 PHE 0.016 0.003 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.38 (12788) covalent geometry : angle 0.83857 / 0.44 (19730) hydrogen bonds : bond 0.10625 / 11.91 ( 461) hydrogen bonds : angle 2.85253 / 3.51 ( 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5741 (mmtt) REVERT: B 5 TYR cc_start: 0.8338 (m-80) cc_final: 0.7993 (m-80) REVERT: B 71 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8033 (pp) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.1291 time to fit residues: 4.8388 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 : 0.148 ------------------------------------------------------------------------------- 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 53 LYS Chi-restraints excluded: chain B residue 71 LEU 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: 20.0000 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.071475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.043714 restraints weight = 59401.084| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.90 r_work: 0.2855 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12788 Z= 0.494 Angle : 0.975 10.125 19730 Z= 0.490 Chirality : 0.066 0.380 2596 Planarity : 0.007 0.037 656 Dihedral : 26.572 179.561 7851 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 7.07 % Allowed : 26.26 % 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: 0.02 (0.80), residues: 114 helix: 0.07 (0.73), residues: 47 sheet: 0.06 (1.02), residues: 28 loop : 0.24 (1.08), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.007 0.002 TYR B 81 PHE 0.015 0.004 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.49 (12788) covalent geometry : angle 0.97521 / 0.49 (19730) hydrogen bonds : bond 0.12201 / 13.65 ( 461) hydrogen bonds : angle 2.92136 / 3.64 ( 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5714 (mmtm) REVERT: B 5 TYR cc_start: 0.8325 (m-80) cc_final: 0.7972 (m-80) REVERT: B 27 GLN cc_start: 0.8966 (mp10) cc_final: 0.8737 (mp10) REVERT: B 71 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8059 (pp) REVERT: B 92 MET cc_start: 0.7886 (ttt) cc_final: 0.7599 (ttt) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 0.1344 time to fit residues: 5.0908 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 : 0.089 ------------------------------------------------------------------------------- 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 53 LYS Chi-restraints excluded: chain B residue 71 LEU 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: 9.9990 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.070428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042387 restraints weight = 60248.015| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.10 r_work: 0.2822 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 12788 Z= 0.637 Angle : 1.224 13.119 19730 Z= 0.592 Chirality : 0.081 0.392 2596 Planarity : 0.008 0.035 656 Dihedral : 26.757 176.198 7851 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 8.08 % Allowed : 24.24 % Favored : 67.68 % 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 (0.77), residues: 114 helix: -0.21 (0.73), residues: 47 sheet: -0.45 (0.98), residues: 28 loop : 0.11 (0.99), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.012 0.003 TYR B 5 PHE 0.018 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00880 / 0.64 (12788) covalent geometry : angle 1.22382 / 0.59 (19730) hydrogen bonds : bond 0.14327 / 15.96 ( 461) hydrogen bonds : angle 3.19140 / 3.99 ( 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.5786 (mmtt) REVERT: B 12 GLU cc_start: 0.8055 (mp0) cc_final: 0.7805 (pm20) REVERT: B 32 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7421 (t) REVERT: B 42 ARG cc_start: 0.8326 (mtm180) cc_final: 0.7929 (mtp85) REVERT: B 71 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8032 (pp) REVERT: B 94 TYR cc_start: 0.7954 (t80) cc_final: 0.7675 (t80) outliers start: 8 outliers final: 4 residues processed: 31 average time/residue: 0.1267 time to fit residues: 5.4197 Evaluate side-chains 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 32 THR Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 50.0000 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.070920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043378 restraints weight = 58350.931| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.47 r_work: 0.2859 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12788 Z= 0.412 Angle : 0.874 9.018 19730 Z= 0.452 Chirality : 0.060 0.360 2596 Planarity : 0.006 0.031 656 Dihedral : 26.696 179.341 7851 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 8.08 % Allowed : 24.24 % Favored : 67.68 % 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: 0.16 (0.78), residues: 114 helix: 0.42 (0.77), residues: 47 sheet: 0.22 (0.98), residues: 26 loop : -0.13 (0.98), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 42 TYR 0.015 0.002 TYR B 40 PHE 0.013 0.003 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.41 (12788) covalent geometry : angle 0.87376 / 0.45 (19730) hydrogen bonds : bond 0.10824 / 12.16 ( 461) hydrogen bonds : angle 2.87137 / 3.63 ( 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5761 (mmtt) REVERT: B 32 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7377 (t) REVERT: B 92 MET cc_start: 0.7877 (ttt) cc_final: 0.7595 (ttt) outliers start: 8 outliers final: 4 residues processed: 29 average time/residue: 0.1225 time to fit residues: 4.9118 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 32 THR Chi-restraints excluded: chain B residue 53 LYS 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: 50.0000 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 4.4144 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.071402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.044135 restraints weight = 59484.957| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.45 r_work: 0.2922 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12788 Z= 0.354 Angle : 0.778 9.384 19730 Z= 0.414 Chirality : 0.054 0.368 2596 Planarity : 0.006 0.032 656 Dihedral : 26.509 179.445 7849 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.06 % Allowed : 25.25 % 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: 0.11 (0.79), residues: 114 helix: 0.26 (0.77), residues: 47 sheet: 0.35 (0.97), residues: 26 loop : -0.10 (1.03), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 35 TYR 0.008 0.002 TYR B 40 PHE 0.011 0.002 PHE B 41 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.35 (12788) covalent geometry : angle 0.77793 / 0.41 (19730) hydrogen bonds : bond 0.10122 / 11.35 ( 461) hydrogen bonds : angle 3.03857 / 3.93 ( 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5887 (mmtt) REVERT: B 92 MET cc_start: 0.7899 (ttt) cc_final: 0.7640 (ttt) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.1261 time to fit residues: 4.7418 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 : 0.109 ------------------------------------------------------------------------------- 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 53 LYS 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: 8.9990 chunk 35 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.070149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042386 restraints weight = 60315.842| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.10 r_work: 0.2821 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 12788 Z= 0.653 Angle : 1.207 13.252 19730 Z= 0.574 Chirality : 0.080 0.399 2596 Planarity : 0.008 0.033 656 Dihedral : 26.565 175.960 7849 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.05 % Allowed : 28.28 % 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: -0.32 (0.80), residues: 114 helix: -0.09 (0.76), residues: 47 sheet: -0.27 (0.98), residues: 28 loop : 0.03 (1.06), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 106 TYR 0.011 0.003 TYR B 40 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 0.00895 / 0.65 (12788) covalent geometry : angle 1.20736 / 0.57 (19730) hydrogen bonds : bond 0.13584 / 15.09 ( 461) hydrogen bonds : angle 3.18461 / 4.14 ( 833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.05 seconds wall clock time: 62 minutes 47.03 seconds (3767.03 seconds total)