Starting phenix.real_space_refine on Mon Feb 10 19:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8okr_16930/02_2025/8okr_16930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8okr_16930/02_2025/8okr_16930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8okr_16930/02_2025/8okr_16930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8okr_16930/02_2025/8okr_16930.map" model { file = "/net/cci-nas-00/data/ceres_data/8okr_16930/02_2025/8okr_16930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8okr_16930/02_2025/8okr_16930.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 1128 2.51 5 N 240 2.21 5 O 216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1608 Number of models: 1 Model: "" Number of chains: 24 Chain: "S" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "T" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "V" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "Q" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Time building chain proxies: 1.28, per 1000 atoms: 0.80 Number of scatterers: 1608 At special positions: 0 Unit cell: (80.19, 54.27, 39.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 216 8.00 N 240 7.00 C 1128 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: 0.96 Conformation dependent library (CDL) restraints added in 133.1 milliseconds 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'T' and resid 3 through 6 removed outlier: 6.220A pdb=" N LYS T 4 " --> pdb=" O PHE N 5 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS N 4 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS H 4 " --> pdb=" O PHE B 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'U' and resid 3 through 6 removed outlier: 5.248A pdb=" N LYS U 4 " --> pdb=" O PHE O 5 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS O 4 " --> pdb=" O PHE I 5 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS I 4 " --> pdb=" O PHE C 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'V' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'W' and resid 3 through 6 removed outlier: 6.220A pdb=" N LYS W 4 " --> pdb=" O PHE Q 5 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS Q 4 " --> pdb=" O PHE K 5 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS K 4 " --> pdb=" O PHE E 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'X' and resid 3 through 6 removed outlier: 5.248A pdb=" N LYS X 4 " --> pdb=" O PHE R 5 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS R 4 " --> pdb=" O PHE L 5 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS L 4 " --> pdb=" O PHE F 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 18 hydrogen bonds defined for protein. 54 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: 0.36 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 216 1.31 - 1.43: 600 1.43 - 1.56: 816 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 1656 Sorted by residual: bond pdb=" C GLN F 6 " pdb=" O GLN F 6 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.14e-02 7.69e+03 2.29e+01 bond pdb=" C GLN C 6 " pdb=" O GLN C 6 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.14e-02 7.69e+03 2.29e+01 bond pdb=" C GLN U 6 " pdb=" O GLN U 6 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.14e-02 7.69e+03 2.28e+01 bond pdb=" C GLN X 6 " pdb=" O GLN X 6 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.14e-02 7.69e+03 2.28e+01 bond pdb=" C GLN L 6 " pdb=" O GLN L 6 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.14e-02 7.69e+03 2.28e+01 ... (remaining 1651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 1832 1.49 - 2.98: 128 2.98 - 4.47: 88 4.47 - 5.97: 56 5.97 - 7.46: 32 Bond angle restraints: 2136 Sorted by residual: angle pdb=" N LYS M 2 " pdb=" CA LYS M 2 " pdb=" C LYS M 2 " ideal model delta sigma weight residual 113.55 107.98 5.57 1.26e+00 6.30e-01 1.95e+01 angle pdb=" N LYS P 2 " pdb=" CA LYS P 2 " pdb=" C LYS P 2 " ideal model delta sigma weight residual 113.55 107.98 5.57 1.26e+00 6.30e-01 1.95e+01 angle pdb=" N LYS G 2 " pdb=" CA LYS G 2 " pdb=" C LYS G 2 " ideal model delta sigma weight residual 113.55 107.98 5.57 1.26e+00 6.30e-01 1.95e+01 angle pdb=" N LYS J 2 " pdb=" CA LYS J 2 " pdb=" C LYS J 2 " ideal model delta sigma weight residual 113.55 107.98 5.57 1.26e+00 6.30e-01 1.95e+01 angle pdb=" N LYS V 2 " pdb=" CA LYS V 2 " pdb=" C LYS V 2 " ideal model delta sigma weight residual 113.55 107.99 5.56 1.26e+00 6.30e-01 1.95e+01 ... (remaining 2131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 752 15.48 - 30.96: 72 30.96 - 46.44: 56 46.44 - 61.93: 48 61.93 - 77.41: 8 Dihedral angle restraints: 936 sinusoidal: 456 harmonic: 480 Sorted by residual: dihedral pdb=" CG LYS A 2 " pdb=" CD LYS A 2 " pdb=" CE LYS A 2 " pdb=" NZ LYS A 2 " ideal model delta sinusoidal sigma weight residual -60.00 -112.89 52.89 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CG LYS D 2 " pdb=" CD LYS D 2 " pdb=" CE LYS D 2 " pdb=" NZ LYS D 2 " ideal model delta sinusoidal sigma weight residual -60.00 -112.89 52.89 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" CG LYS V 2 " pdb=" CD LYS V 2 " pdb=" CE LYS V 2 " pdb=" NZ LYS V 2 " ideal model delta sinusoidal sigma weight residual -60.00 -112.88 52.88 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 933 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.036: 48 0.036 - 0.070: 10 0.070 - 0.105: 54 0.105 - 0.140: 40 0.140 - 0.175: 16 Chirality restraints: 168 Sorted by residual: chirality pdb=" CA LYS I 4 " pdb=" N LYS I 4 " pdb=" C LYS I 4 " pdb=" CB LYS I 4 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA LYS L 4 " pdb=" N LYS L 4 " pdb=" C LYS L 4 " pdb=" CB LYS L 4 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA LYS X 4 " pdb=" N LYS X 4 " pdb=" C LYS X 4 " pdb=" CB LYS X 4 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 165 not shown) Planarity restraints: 264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS H 1 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C CYS H 1 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS H 1 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS H 2 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS Q 1 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C CYS Q 1 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS Q 1 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS Q 2 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 1 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C CYS K 1 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS K 1 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS K 2 " -0.012 2.00e-02 2.50e+03 ... (remaining 261 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 6 2.17 - 2.85: 530 2.85 - 3.54: 1944 3.54 - 4.22: 3632 4.22 - 4.90: 7220 Nonbonded interactions: 13332 Sorted by model distance: nonbonded pdb=" NZ LYS Q 4 " pdb=" O PHE J 7 " model vdw 1.489 3.120 nonbonded pdb=" NZ LYS N 4 " pdb=" O PHE G 7 " model vdw 1.489 3.120 nonbonded pdb=" NZ LYS T 4 " pdb=" O PHE M 7 " model vdw 1.490 3.120 nonbonded pdb=" NZ LYS W 4 " pdb=" O PHE P 7 " model vdw 1.490 3.120 nonbonded pdb=" NZ LYS H 4 " pdb=" O PHE A 7 " model vdw 1.490 3.120 ... (remaining 13327 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.040 Find NCS groups from input model: 0.090 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 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 : 0.007 0.055 1656 Z= 0.415 Angle : 1.558 7.456 2136 Z= 0.983 Chirality : 0.091 0.175 168 Planarity : 0.005 0.020 264 Dihedral : 22.908 77.407 600 Min Nonbonded Distance : 1.489 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.40), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.30), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE M 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.205 Fit side-chains REVERT: U 2 LYS cc_start: 0.4947 (mmtt) cc_final: 0.3714 (pptt) REVERT: X 2 LYS cc_start: 0.4945 (mmtt) cc_final: 0.3714 (pptt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 2.2044 time to fit residues: 18.0862 Evaluate side-chains 2 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 6 GLN X 6 GLN O 6 GLN R 6 GLN I 6 GLN L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.083755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055450 restraints weight = 3409.253| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.73 r_work: 0.2830 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.9462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.187 0.560 1656 Z=10.705 Angle : 6.365 33.748 2136 Z= 3.423 Chirality : 0.431 0.835 168 Planarity : 0.039 0.094 264 Dihedral : 25.897 78.065 168 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 137.64 Ramachandran Plot: Outliers : 21.67 % Allowed : 23.33 % Favored : 55.00 % Rotamer: Outliers : 7.14 % Allowed : 22.62 % Favored : 70.24 % Cbeta Deviations : 32.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.94 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.73 (0.36), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.89 (0.28), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.106 0.021 PHE K 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7817 (tppp) REVERT: R 2 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7823 (tppp) REVERT: H 2 LYS cc_start: 0.8677 (tttt) cc_final: 0.8172 (ttmp) REVERT: I 2 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8297 (mtpt) REVERT: I 4 LYS cc_start: 0.9161 (mttp) cc_final: 0.8775 (mttt) REVERT: K 2 LYS cc_start: 0.8677 (tttt) cc_final: 0.8173 (ttmp) REVERT: L 2 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8303 (mtpt) REVERT: L 4 LYS cc_start: 0.9162 (mttp) cc_final: 0.8776 (mttt) outliers start: 12 outliers final: 4 residues processed: 32 average time/residue: 1.8188 time to fit residues: 58.9445 Evaluate side-chains 36 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3471 r_free = 0.3471 target = 0.082436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.054669 restraints weight = 3630.213| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.80 r_work: 0.2818 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 1.0354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.554 1656 Z=10.851 Angle : 6.349 32.854 2136 Z= 3.453 Chirality : 0.432 0.796 168 Planarity : 0.038 0.087 264 Dihedral : 29.815 80.851 168 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 147.86 Ramachandran Plot: Outliers : 13.33 % Allowed : 41.67 % Favored : 45.00 % Rotamer: Outliers : 10.71 % Allowed : 30.36 % Favored : 58.93 % Cbeta Deviations : 36.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.74 (0.43), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.90 (0.33), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.112 0.020 PHE X 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 6 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: U 7 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: X 6 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8737 (mt0) REVERT: X 7 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: O 2 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7879 (tppp) REVERT: O 6 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: R 2 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7877 (tppp) REVERT: R 6 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8361 (mt0) REVERT: H 2 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8421 (ttmp) REVERT: I 2 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8394 (mmtp) REVERT: I 4 LYS cc_start: 0.9290 (mttt) cc_final: 0.8902 (mttt) REVERT: K 2 LYS cc_start: 0.8751 (tttt) cc_final: 0.8365 (ttmp) REVERT: L 2 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8390 (mmtp) REVERT: L 4 LYS cc_start: 0.9287 (mttt) cc_final: 0.8897 (mttt) outliers start: 18 outliers final: 6 residues processed: 32 average time/residue: 2.0036 time to fit residues: 64.9337 Evaluate side-chains 42 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 7 PHE Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3506 r_free = 0.3506 target = 0.083860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054134 restraints weight = 3471.478| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.94 r_work: 0.2808 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 1.0500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.555 1656 Z=10.873 Angle : 6.370 33.892 2136 Z= 3.467 Chirality : 0.433 0.784 168 Planarity : 0.038 0.087 264 Dihedral : 30.316 89.330 168 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 147.59 Ramachandran Plot: Outliers : 12.50 % Allowed : 43.33 % Favored : 44.17 % Rotamer: Outliers : 16.67 % Allowed : 20.24 % Favored : 63.10 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.74 (0.45), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.90 (0.35), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.083 0.020 PHE P 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 23 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8796 (mtpt) REVERT: U 7 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: W 4 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8809 (mtpt) REVERT: X 6 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: X 7 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: O 2 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7784 (tppp) REVERT: R 2 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7782 (tppp) REVERT: H 2 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8401 (ttmp) REVERT: I 2 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8239 (mmtp) REVERT: I 4 LYS cc_start: 0.9279 (mttp) cc_final: 0.8872 (mttt) REVERT: K 2 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8349 (ttmp) REVERT: L 2 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8261 (mmtp) REVERT: L 4 LYS cc_start: 0.9280 (mttp) cc_final: 0.8870 (mttt) REVERT: B 4 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8852 (mtpt) REVERT: C 4 LYS cc_start: 0.9257 (mttp) cc_final: 0.8907 (mttp) REVERT: E 4 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8914 (mtpt) REVERT: F 4 LYS cc_start: 0.9255 (mttp) cc_final: 0.8897 (mttp) outliers start: 28 outliers final: 11 residues processed: 38 average time/residue: 2.0286 time to fit residues: 77.9515 Evaluate side-chains 45 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 23 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 7 PHE Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3507 r_free = 0.3507 target = 0.083337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.055105 restraints weight = 3664.885| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.03 r_work: 0.2820 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 1.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.559 1656 Z=10.863 Angle : 6.392 33.989 2136 Z= 3.476 Chirality : 0.432 0.779 168 Planarity : 0.038 0.086 264 Dihedral : 30.345 86.112 168 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 145.45 Ramachandran Plot: Outliers : 10.00 % Allowed : 48.33 % Favored : 41.67 % Rotamer: Outliers : 15.48 % Allowed : 20.24 % Favored : 64.29 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.74 (0.47), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.90 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.091 0.020 PHE X 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 22 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8859 (mtpt) REVERT: U 7 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: W 4 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8894 (mtpt) REVERT: X 6 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8440 (mt0) REVERT: X 7 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: O 2 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7778 (tppp) REVERT: R 2 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7782 (tppp) REVERT: H 2 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8321 (ttmp) REVERT: I 2 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8259 (mmtp) REVERT: I 4 LYS cc_start: 0.9252 (mttp) cc_final: 0.8787 (mttt) REVERT: K 2 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8322 (ttmp) REVERT: L 2 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8289 (mmtp) REVERT: L 4 LYS cc_start: 0.9253 (mttp) cc_final: 0.8791 (mttt) REVERT: B 4 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8876 (mtpt) REVERT: C 4 LYS cc_start: 0.9246 (mttp) cc_final: 0.8875 (mttp) REVERT: E 4 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8910 (mtpt) REVERT: F 4 LYS cc_start: 0.9245 (mttp) cc_final: 0.8875 (mttp) outliers start: 26 outliers final: 9 residues processed: 35 average time/residue: 1.9882 time to fit residues: 70.3856 Evaluate side-chains 42 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 22 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain U residue 7 PHE Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 7 PHE Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3497 r_free = 0.3497 target = 0.082780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054569 restraints weight = 3574.784| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.85 r_work: 0.2828 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 1.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.561 1656 Z=10.880 Angle : 6.394 33.610 2136 Z= 3.476 Chirality : 0.432 0.781 168 Planarity : 0.038 0.087 264 Dihedral : 30.490 87.465 168 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 148.36 Ramachandran Plot: Outliers : 10.00 % Allowed : 48.33 % Favored : 41.67 % Rotamer: Outliers : 13.10 % Allowed : 24.40 % Favored : 62.50 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.73 (0.47), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.89 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.087 0.020 PHE X 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 18 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8840 (mtpt) REVERT: W 4 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8840 (mtpt) REVERT: X 6 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8524 (mt0) REVERT: O 2 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7923 (tppp) REVERT: R 2 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7931 (tppp) REVERT: I 2 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8339 (mmtp) REVERT: I 4 LYS cc_start: 0.9290 (mttp) cc_final: 0.8835 (mttt) REVERT: L 2 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8341 (mmtp) REVERT: L 4 LYS cc_start: 0.9296 (mttp) cc_final: 0.8847 (mttt) REVERT: B 4 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8842 (mtpt) REVERT: C 4 LYS cc_start: 0.9278 (mttp) cc_final: 0.8920 (mttp) REVERT: E 4 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8908 (mtpt) REVERT: F 4 LYS cc_start: 0.9278 (mttp) cc_final: 0.8927 (mttp) outliers start: 22 outliers final: 9 residues processed: 30 average time/residue: 1.9573 time to fit residues: 59.5233 Evaluate side-chains 36 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3499 r_free = 0.3499 target = 0.082742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054577 restraints weight = 3582.651| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.81 r_work: 0.2825 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 1.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.559 1656 Z=10.885 Angle : 6.405 35.552 2136 Z= 3.481 Chirality : 0.433 0.783 168 Planarity : 0.038 0.087 264 Dihedral : 30.654 89.194 168 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 149.42 Ramachandran Plot: Outliers : 10.00 % Allowed : 48.33 % Favored : 41.67 % Rotamer: Outliers : 13.10 % Allowed : 26.19 % Favored : 60.71 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.77 (0.46), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.92 (0.35), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.085 0.020 PHE M 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 18 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8895 (mtpt) REVERT: W 4 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8897 (mtpt) REVERT: O 2 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7943 (tppp) REVERT: R 2 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7951 (tppp) REVERT: I 2 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8360 (mmtp) REVERT: I 4 LYS cc_start: 0.9296 (mttp) cc_final: 0.8844 (mttt) REVERT: L 2 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8364 (mmtp) REVERT: L 4 LYS cc_start: 0.9301 (mttp) cc_final: 0.8854 (mttt) REVERT: B 4 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8878 (mtpt) REVERT: C 4 LYS cc_start: 0.9295 (mttp) cc_final: 0.8928 (mttp) REVERT: E 4 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8912 (mtpt) REVERT: F 4 LYS cc_start: 0.9295 (mttp) cc_final: 0.8942 (mttp) outliers start: 22 outliers final: 12 residues processed: 30 average time/residue: 1.9165 time to fit residues: 58.2545 Evaluate side-chains 38 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3495 r_free = 0.3495 target = 0.082649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.054539 restraints weight = 3512.541| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.82 r_work: 0.2826 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 1.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.557 1656 Z=10.883 Angle : 6.412 35.417 2136 Z= 3.485 Chirality : 0.432 0.779 168 Planarity : 0.038 0.087 264 Dihedral : 30.630 88.760 168 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 148.26 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 11.90 % Allowed : 26.19 % Favored : 61.90 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.76 (0.47), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.020 PHE P 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8883 (mtpt) REVERT: W 4 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8879 (mtpt) REVERT: X 6 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: O 2 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7918 (tppp) REVERT: R 2 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7929 (tppp) REVERT: I 2 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8336 (mmtp) REVERT: I 4 LYS cc_start: 0.9293 (mttp) cc_final: 0.8837 (mttt) REVERT: L 2 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8343 (mmtp) REVERT: L 4 LYS cc_start: 0.9297 (mttp) cc_final: 0.8848 (mttt) REVERT: B 4 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8838 (mtpt) REVERT: C 4 LYS cc_start: 0.9294 (mttp) cc_final: 0.8929 (mttp) REVERT: E 4 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8910 (mtpt) REVERT: F 4 LYS cc_start: 0.9293 (mttp) cc_final: 0.8936 (mttp) outliers start: 20 outliers final: 11 residues processed: 28 average time/residue: 2.1320 time to fit residues: 60.4108 Evaluate side-chains 38 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3493 r_free = 0.3493 target = 0.082575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054431 restraints weight = 3574.787| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.84 r_work: 0.2824 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 1.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.560 1656 Z=10.883 Angle : 6.413 35.485 2136 Z= 3.486 Chirality : 0.432 0.778 168 Planarity : 0.038 0.087 264 Dihedral : 30.629 88.954 168 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 148.89 Ramachandran Plot: Outliers : 10.00 % Allowed : 48.33 % Favored : 41.67 % Rotamer: Outliers : 11.90 % Allowed : 26.19 % Favored : 61.90 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.76 (0.46), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.35), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.020 PHE P 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8882 (mtpt) REVERT: W 4 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8882 (mtpt) REVERT: X 6 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8515 (mt0) REVERT: O 2 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7918 (tppp) REVERT: R 2 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7927 (tppp) REVERT: I 2 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8337 (mmtp) REVERT: I 4 LYS cc_start: 0.9291 (mttp) cc_final: 0.8833 (mttt) REVERT: L 2 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8343 (mmtp) REVERT: L 4 LYS cc_start: 0.9297 (mttp) cc_final: 0.8850 (mttt) REVERT: B 4 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8866 (mtpt) REVERT: C 4 LYS cc_start: 0.9281 (mttp) cc_final: 0.8915 (mttp) REVERT: E 4 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8907 (mtpt) REVERT: F 4 LYS cc_start: 0.9294 (mttp) cc_final: 0.8938 (mttp) outliers start: 20 outliers final: 11 residues processed: 28 average time/residue: 2.0097 time to fit residues: 57.0442 Evaluate side-chains 38 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3493 r_free = 0.3493 target = 0.082572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054350 restraints weight = 3629.449| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.87 r_work: 0.2822 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 1.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.560 1656 Z=10.884 Angle : 6.412 35.424 2136 Z= 3.485 Chirality : 0.432 0.779 168 Planarity : 0.038 0.087 264 Dihedral : 30.625 88.867 168 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 149.20 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 11.90 % Allowed : 26.19 % Favored : 61.90 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.76 (0.46), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.35), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.020 PHE P 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8884 (mtpt) REVERT: W 4 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8882 (mtpt) REVERT: X 6 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: O 2 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7920 (tppp) REVERT: R 2 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7930 (tppp) REVERT: I 2 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8337 (mmtp) REVERT: I 4 LYS cc_start: 0.9291 (mttp) cc_final: 0.8834 (mttt) REVERT: L 2 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8343 (mmtp) REVERT: L 4 LYS cc_start: 0.9296 (mttp) cc_final: 0.8847 (mttt) REVERT: B 4 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8840 (mtpt) REVERT: C 4 LYS cc_start: 0.9281 (mttp) cc_final: 0.8915 (mttp) REVERT: E 4 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8912 (mtpt) REVERT: F 4 LYS cc_start: 0.9294 (mttp) cc_final: 0.8938 (mttp) outliers start: 20 outliers final: 11 residues processed: 28 average time/residue: 1.9916 time to fit residues: 56.4440 Evaluate side-chains 38 residues out of total 168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 2 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain F residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.3493 r_free = 0.3493 target = 0.082566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.054240 restraints weight = 3704.665| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.90 r_work: 0.2820 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 1.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.560 1656 Z=10.883 Angle : 6.412 35.435 2136 Z= 3.486 Chirality : 0.432 0.778 168 Planarity : 0.038 0.087 264 Dihedral : 30.626 88.884 168 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 149.52 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 11.90 % Allowed : 26.19 % Favored : 61.90 % Cbeta Deviations : 38.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.76 (0.46), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.35), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.020 PHE P 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1306.20 seconds wall clock time: 24 minutes 7.85 seconds (1447.85 seconds total)