Starting phenix.real_space_refine on Tue Aug 4 12:43:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w09_65499/08_2026/9w09_65499.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w09_65499/08_2026/9w09_65499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w09_65499/08_2026/9w09_65499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w09_65499/08_2026/9w09_65499.map" model { file = "/net/cci-nas-00/data/ceres_data/9w09_65499/08_2026/9w09_65499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w09_65499/08_2026/9w09_65499.cif" } resolution = 3.1 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= 0.002 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: 3 Type Number sf(0) Gaussians C 1824 2.51 5 N 510 2.21 5 O 582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 2916 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 446 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: M, N, R, S, T, P, Q, U, V, W Time building chain proxies: 0.62, per 1000 atoms: 0.21 Number of scatterers: 2916 At special positions: 0 Unit cell: (100.43, 136.95, 32.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 582 8.00 N 510 7.00 C 1824 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: 0.22 Conformation dependent library (CDL) restraints added in 119.9 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'O' and resid 39 through 40 removed outlier: 6.401A pdb=" N TYR O 39 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 46 through 50 removed outlier: 6.917A pdb=" N GLY O 47 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU P 46 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N VAL Q 49 " --> pdb=" O GLU P 46 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL P 48 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 55 through 65 removed outlier: 8.911A pdb=" N VAL O 55 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N LYS Q 58 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N GLU O 57 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N LYS Q 60 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR O 59 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLN Q 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU O 61 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR Q 64 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL O 63 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA P 56 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU Q 57 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS P 58 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR Q 59 " --> pdb=" O LYS P 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 70 through 71 removed outlier: 6.465A pdb=" N VAL O 70 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 75 through 78 Processing sheet with id=AA6, first strand: chain 'O' and resid 82 through 83 removed outlier: 6.605A pdb=" N VAL P 82 " --> pdb=" O GLU Q 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 88 through 89 removed outlier: 6.699A pdb=" N ILE O 88 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 94 through 96 removed outlier: 6.610A pdb=" N VAL P 95 " --> pdb=" O LYS Q 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 39 through 40 removed outlier: 6.401A pdb=" N TYR U 39 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 46 through 50 removed outlier: 6.917A pdb=" N GLY U 47 " --> pdb=" O GLU W 46 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU V 46 " --> pdb=" O GLY W 47 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N VAL W 49 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL V 48 " --> pdb=" O VAL W 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 55 through 65 removed outlier: 8.911A pdb=" N VAL U 55 " --> pdb=" O ALA W 56 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N LYS W 58 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N GLU U 57 " --> pdb=" O LYS W 58 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N LYS W 60 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR U 59 " --> pdb=" O LYS W 60 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLN W 62 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU U 61 " --> pdb=" O GLN W 62 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR W 64 " --> pdb=" O GLU U 61 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL U 63 " --> pdb=" O THR W 64 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA V 56 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU W 57 " --> pdb=" O ALA V 56 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS V 58 " --> pdb=" O GLU W 57 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR W 59 " --> pdb=" O LYS V 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 70 through 71 removed outlier: 6.465A pdb=" N VAL U 70 " --> pdb=" O VAL W 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 75 through 78 Processing sheet with id=AB5, first strand: chain 'U' and resid 82 through 83 removed outlier: 6.606A pdb=" N VAL V 82 " --> pdb=" O GLU W 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 88 through 89 removed outlier: 6.699A pdb=" N ILE U 88 " --> pdb=" O ALA W 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 94 through 96 removed outlier: 6.610A pdb=" N VAL V 95 " --> pdb=" O LYS W 96 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 516 1.29 - 1.35: 456 1.35 - 1.41: 106 1.41 - 1.48: 482 1.48 - 1.54: 1362 Bond restraints: 2922 Sorted by residual: bond pdb=" CA GLY W 73 " pdb=" C GLY W 73 " ideal model delta sigma weight residual 1.519 1.510 0.009 8.90e-03 1.26e+04 1.04e+00 bond pdb=" CA GLY Q 73 " pdb=" C GLY Q 73 " ideal model delta sigma weight residual 1.519 1.510 0.009 8.90e-03 1.26e+04 9.49e-01 bond pdb=" CA VAL U 66 " pdb=" CB VAL U 66 " ideal model delta sigma weight residual 1.545 1.537 0.009 9.10e-03 1.21e+04 8.93e-01 bond pdb=" CA VAL O 66 " pdb=" CB VAL O 66 " ideal model delta sigma weight residual 1.545 1.537 0.009 9.10e-03 1.21e+04 8.88e-01 bond pdb=" CA VAL V 66 " pdb=" CB VAL V 66 " ideal model delta sigma weight residual 1.545 1.537 0.008 9.10e-03 1.21e+04 8.39e-01 ... (remaining 2917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 3042 0.77 - 1.54: 704 1.54 - 2.31: 174 2.31 - 3.08: 22 3.08 - 3.85: 12 Bond angle restraints: 3954 Sorted by residual: angle pdb=" C ASN Q 65 " pdb=" N VAL Q 66 " pdb=" CA VAL Q 66 " ideal model delta sigma weight residual 122.97 120.16 2.81 9.80e-01 1.04e+00 8.22e+00 angle pdb=" C ASN W 65 " pdb=" N VAL W 66 " pdb=" CA VAL W 66 " ideal model delta sigma weight residual 122.97 120.19 2.78 9.80e-01 1.04e+00 8.05e+00 angle pdb=" C ASN V 65 " pdb=" N VAL V 66 " pdb=" CA VAL V 66 " ideal model delta sigma weight residual 122.97 120.20 2.77 9.80e-01 1.04e+00 7.97e+00 angle pdb=" C ASN U 65 " pdb=" N VAL U 66 " pdb=" CA VAL U 66 " ideal model delta sigma weight residual 122.97 120.22 2.75 9.80e-01 1.04e+00 7.90e+00 angle pdb=" C ASN O 65 " pdb=" N VAL O 66 " pdb=" CA VAL O 66 " ideal model delta sigma weight residual 122.97 120.24 2.73 9.80e-01 1.04e+00 7.78e+00 ... (remaining 3949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.59: 1530 12.59 - 25.19: 138 25.19 - 37.78: 24 37.78 - 50.38: 18 50.38 - 62.97: 6 Dihedral angle restraints: 1716 sinusoidal: 534 harmonic: 1182 Sorted by residual: dihedral pdb=" CA LYS O 80 " pdb=" CB LYS O 80 " pdb=" CG LYS O 80 " pdb=" CD LYS O 80 " ideal model delta sinusoidal sigma weight residual -60.00 -98.91 38.91 3 1.50e+01 4.44e-03 6.87e+00 dihedral pdb=" CA LYS Q 80 " pdb=" CB LYS Q 80 " pdb=" CG LYS Q 80 " pdb=" CD LYS Q 80 " ideal model delta sinusoidal sigma weight residual -60.00 -98.91 38.91 3 1.50e+01 4.44e-03 6.87e+00 dihedral pdb=" CA LYS W 80 " pdb=" CB LYS W 80 " pdb=" CG LYS W 80 " pdb=" CD LYS W 80 " ideal model delta sinusoidal sigma weight residual -60.00 -98.89 38.89 3 1.50e+01 4.44e-03 6.87e+00 ... (remaining 1713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 246 0.029 - 0.058: 160 0.058 - 0.087: 50 0.087 - 0.117: 61 0.117 - 0.146: 11 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ILE Q 88 " pdb=" N ILE Q 88 " pdb=" C ILE Q 88 " pdb=" CB ILE Q 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE O 88 " pdb=" N ILE O 88 " pdb=" C ILE O 88 " pdb=" CB ILE O 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE V 88 " pdb=" N ILE V 88 " pdb=" C ILE V 88 " pdb=" CB ILE V 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 525 not shown) Planarity restraints: 492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY P 84 " -0.004 2.00e-02 2.50e+03 7.51e-03 5.63e-01 pdb=" C GLY P 84 " 0.013 2.00e-02 2.50e+03 pdb=" O GLY P 84 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA P 85 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY V 84 " 0.004 2.00e-02 2.50e+03 7.14e-03 5.10e-01 pdb=" C GLY V 84 " -0.012 2.00e-02 2.50e+03 pdb=" O GLY V 84 " 0.005 2.00e-02 2.50e+03 pdb=" N ALA V 85 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY U 84 " 0.004 2.00e-02 2.50e+03 7.14e-03 5.10e-01 pdb=" C GLY U 84 " -0.012 2.00e-02 2.50e+03 pdb=" O GLY U 84 " 0.005 2.00e-02 2.50e+03 pdb=" N ALA U 85 " 0.004 2.00e-02 2.50e+03 ... (remaining 489 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1322 2.95 - 3.44: 2492 3.44 - 3.92: 4244 3.92 - 4.41: 4645 4.41 - 4.90: 9734 Nonbonded interactions: 22437 Sorted by model distance: nonbonded pdb=" NZ LYS P 96 " pdb=" OD2 ASP P 98 " model vdw 2.459 3.120 nonbonded pdb=" NZ LYS V 96 " pdb=" OD2 ASP V 98 " model vdw 2.459 3.120 nonbonded pdb=" NZ LYS O 96 " pdb=" OD2 ASP O 98 " model vdw 2.459 3.120 nonbonded pdb=" NZ LYS U 96 " pdb=" OD2 ASP U 98 " model vdw 2.459 3.120 nonbonded pdb=" NZ LYS W 96 " pdb=" OD2 ASP W 98 " model vdw 2.459 3.120 ... (remaining 22432 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: 0.01 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.006 0.023 2922 Z= 0.296 Angle : 0.722 3.851 3954 Z= 0.446 Chirality : 0.050 0.146 528 Planarity : 0.002 0.008 492 Dihedral : 12.688 62.969 960 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.33), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR O 39 PHE 0.006 0.002 PHE O 94 HIS 0.003 0.002 HIS Q 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.30 ( 2922) covalent geometry : angle 0.72234 / 0.45 ( 3954) hydrogen bonds : bond 0.11729 / 5.93 ( 42) hydrogen bonds : angle 7.19410 / 4.28 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0474 time to fit residues: 1.4141 Evaluate side-chains 15 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 50 HIS O 79 GLN P 50 HIS P 79 GLN Q 50 HIS Q 79 GLN U 50 HIS U 79 GLN V 50 HIS V 79 GLN W 50 HIS W 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.156168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.115683 restraints weight = 3064.522| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.42 r_work: 0.3950 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2922 Z= 0.201 Angle : 0.529 3.391 3954 Z= 0.297 Chirality : 0.050 0.146 528 Planarity : 0.002 0.009 492 Dihedral : 4.758 15.480 426 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.17 % Allowed : 11.96 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.35), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR P 39 PHE 0.007 0.002 PHE V 94 HIS 0.002 0.001 HIS P 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 ( 2922) covalent geometry : angle 0.52930 / 0.30 ( 3954) hydrogen bonds : bond 0.02111 / 1.15 ( 42) hydrogen bonds : angle 5.30959 / 3.25 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.112 Fit side-chains REVERT: P 99 GLN cc_start: 0.6895 (mp10) cc_final: 0.6537 (mp10) REVERT: W 87 SER cc_start: 0.8955 (p) cc_final: 0.8730 (p) outliers start: 6 outliers final: 6 residues processed: 21 average time/residue: 0.0313 time to fit residues: 1.1110 Evaluate side-chains 19 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.147927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.108234 restraints weight = 3181.449| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.43 r_work: 0.3739 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2922 Z= 0.281 Angle : 0.594 3.623 3954 Z= 0.335 Chirality : 0.052 0.136 528 Planarity : 0.002 0.010 492 Dihedral : 5.038 14.582 426 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.62 % Allowed : 11.23 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.36), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR V 39 PHE 0.006 0.001 PHE U 94 HIS 0.002 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 ( 2922) covalent geometry : angle 0.59373 / 0.34 ( 3954) hydrogen bonds : bond 0.02294 / 1.19 ( 42) hydrogen bonds : angle 4.95887 / 2.92 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.099 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 26 average time/residue: 0.0290 time to fit residues: 1.1932 Evaluate side-chains 26 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 99 GLN P 99 GLN Q 99 GLN U 62 GLN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.149047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.109291 restraints weight = 3103.656| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.37 r_work: 0.3752 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2922 Z= 0.229 Angle : 0.535 3.368 3954 Z= 0.302 Chirality : 0.051 0.134 528 Planarity : 0.002 0.012 492 Dihedral : 4.720 14.461 426 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.88 % Allowed : 11.59 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.37), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR W 39 PHE 0.006 0.002 PHE Q 94 HIS 0.002 0.001 HIS W 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 ( 2922) covalent geometry : angle 0.53489 / 0.30 ( 3954) hydrogen bonds : bond 0.01566 / 0.83 ( 42) hydrogen bonds : angle 4.71432 / 2.78 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 15 time to evaluate : 0.105 Fit side-chains REVERT: O 38 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8064 (tt) REVERT: Q 38 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8057 (tt) REVERT: U 38 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8411 (tt) REVERT: W 38 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7906 (tt) outliers start: 19 outliers final: 14 residues processed: 32 average time/residue: 0.0306 time to fit residues: 1.5235 Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 15 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 62 GLN P 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.152435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.112024 restraints weight = 2954.272| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.38 r_work: 0.3924 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2922 Z= 0.130 Angle : 0.435 3.195 3954 Z= 0.245 Chirality : 0.049 0.127 528 Planarity : 0.001 0.006 492 Dihedral : 4.282 12.974 426 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.43 % Allowed : 12.68 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.38), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR Q 39 PHE 0.006 0.001 PHE Q 94 HIS 0.001 0.001 HIS W 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 2922) covalent geometry : angle 0.43502 / 0.24 ( 3954) hydrogen bonds : bond 0.01192 / 0.63 ( 42) hydrogen bonds : angle 4.42069 / 2.60 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 18 time to evaluate : 0.062 Fit side-chains REVERT: P 99 GLN cc_start: 0.6844 (mp10) cc_final: 0.6643 (mp10) REVERT: Q 38 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8039 (tt) REVERT: V 38 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8263 (tt) outliers start: 15 outliers final: 13 residues processed: 29 average time/residue: 0.0249 time to fit residues: 1.1154 Evaluate side-chains 32 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 99 GLN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.150040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.110301 restraints weight = 3076.422| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.31 r_work: 0.3782 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2922 Z= 0.173 Angle : 0.472 3.458 3954 Z= 0.264 Chirality : 0.049 0.129 528 Planarity : 0.002 0.005 492 Dihedral : 4.379 13.402 426 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.88 % Allowed : 11.23 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.38), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR W 39 PHE 0.006 0.002 PHE Q 94 HIS 0.002 0.001 HIS V 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 2922) covalent geometry : angle 0.47176 / 0.26 ( 3954) hydrogen bonds : bond 0.01299 / 0.69 ( 42) hydrogen bonds : angle 4.48906 / 2.62 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 16 time to evaluate : 0.102 Fit side-chains REVERT: O 38 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8046 (tt) REVERT: P 99 GLN cc_start: 0.6902 (mp10) cc_final: 0.6692 (mp10) REVERT: Q 38 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8044 (tt) REVERT: V 38 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8232 (tt) REVERT: W 38 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7917 (tt) outliers start: 19 outliers final: 14 residues processed: 29 average time/residue: 0.0302 time to fit residues: 1.3708 Evaluate side-chains 34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 16 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 99 GLN Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.173119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.134923 restraints weight = 3047.319| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.07 r_work: 0.3908 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2922 Z= 0.075 Angle : 0.383 3.107 3954 Z= 0.214 Chirality : 0.048 0.123 528 Planarity : 0.001 0.004 492 Dihedral : 3.884 11.626 426 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 4.71 % Allowed : 13.04 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR U 39 PHE 0.006 0.001 PHE W 94 HIS 0.000 0.000 HIS U 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.08 ( 2922) covalent geometry : angle 0.38327 / 0.21 ( 3954) hydrogen bonds : bond 0.00945 / 0.50 ( 42) hydrogen bonds : angle 4.16872 / 2.44 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.100 Fit side-chains REVERT: P 99 GLN cc_start: 0.6696 (mp10) cc_final: 0.6445 (mp10) REVERT: V 97 LYS cc_start: 0.7537 (ptmt) cc_final: 0.7108 (ptpp) REVERT: W 38 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7909 (tt) outliers start: 13 outliers final: 10 residues processed: 28 average time/residue: 0.0399 time to fit residues: 1.5903 Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 19 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 99 GLN Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.172362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.133651 restraints weight = 3110.299| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.12 r_work: 0.3891 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2922 Z= 0.085 Angle : 0.392 4.195 3954 Z= 0.216 Chirality : 0.048 0.124 528 Planarity : 0.001 0.009 492 Dihedral : 3.771 11.719 426 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.71 % Allowed : 13.04 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR O 39 PHE 0.006 0.001 PHE W 94 HIS 0.001 0.000 HIS P 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 ( 2922) covalent geometry : angle 0.39211 / 0.22 ( 3954) hydrogen bonds : bond 0.00909 / 0.49 ( 42) hydrogen bonds : angle 4.09096 / 2.39 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.102 Fit side-chains REVERT: P 99 GLN cc_start: 0.6744 (mp10) cc_final: 0.6444 (mp10) REVERT: Q 38 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8088 (tt) REVERT: V 38 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8267 (tt) REVERT: V 97 LYS cc_start: 0.7545 (ptmt) cc_final: 0.7125 (ptpp) REVERT: W 38 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8003 (tt) outliers start: 13 outliers final: 10 residues processed: 28 average time/residue: 0.0401 time to fit residues: 1.5988 Evaluate side-chains 33 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 99 GLN Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 GLN ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.147788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.108079 restraints weight = 3148.117| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.36 r_work: 0.3751 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2922 Z= 0.244 Angle : 0.533 3.962 3954 Z= 0.294 Chirality : 0.050 0.132 528 Planarity : 0.002 0.010 492 Dihedral : 4.430 13.149 426 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 6.16 % Allowed : 11.96 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR O 39 PHE 0.006 0.001 PHE U 94 HIS 0.002 0.001 HIS W 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 ( 2922) covalent geometry : angle 0.53312 / 0.29 ( 3954) hydrogen bonds : bond 0.01456 / 0.76 ( 42) hydrogen bonds : angle 4.40196 / 2.55 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 14 time to evaluate : 0.096 Fit side-chains REVERT: P 99 GLN cc_start: 0.6838 (mp10) cc_final: 0.6555 (mp10) REVERT: Q 38 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8091 (tt) REVERT: V 38 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8228 (tt) REVERT: V 97 LYS cc_start: 0.7626 (ptmt) cc_final: 0.7243 (ptpp) REVERT: W 38 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7939 (tt) outliers start: 17 outliers final: 13 residues processed: 27 average time/residue: 0.0362 time to fit residues: 1.4341 Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 14 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 99 GLN Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.0470 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.169362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.131106 restraints weight = 3119.769| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.10 r_work: 0.3857 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2922 Z= 0.103 Angle : 0.418 4.125 3954 Z= 0.229 Chirality : 0.048 0.123 528 Planarity : 0.001 0.004 492 Dihedral : 3.943 11.888 426 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.07 % Allowed : 13.04 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.40), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR O 39 PHE 0.006 0.001 PHE Q 94 HIS 0.001 0.000 HIS P 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 2922) covalent geometry : angle 0.41801 / 0.23 ( 3954) hydrogen bonds : bond 0.01039 / 0.55 ( 42) hydrogen bonds : angle 4.15993 / 2.43 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 16 time to evaluate : 0.100 Fit side-chains REVERT: P 99 GLN cc_start: 0.6703 (mp10) cc_final: 0.6436 (mp10) REVERT: Q 38 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8142 (tt) REVERT: V 38 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8245 (tt) REVERT: W 38 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7968 (tt) outliers start: 14 outliers final: 11 residues processed: 26 average time/residue: 0.0382 time to fit residues: 1.4367 Evaluate side-chains 30 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 16 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 44 THR Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 99 GLN Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.0050 overall best weight: 2.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.149100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.109576 restraints weight = 3062.191| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.28 r_work: 0.3884 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2922 Z= 0.172 Angle : 0.471 4.272 3954 Z= 0.259 Chirality : 0.049 0.129 528 Planarity : 0.001 0.005 492 Dihedral : 4.170 12.650 426 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.07 % Allowed : 12.68 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.40), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR O 39 PHE 0.006 0.001 PHE Q 94 HIS 0.001 0.001 HIS W 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 2922) covalent geometry : angle 0.47148 / 0.26 ( 3954) hydrogen bonds : bond 0.01232 / 0.65 ( 42) hydrogen bonds : angle 4.24465 / 2.45 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1014.96 seconds wall clock time: 17 minutes 59.04 seconds (1079.04 seconds total)