Starting phenix.real_space_refine on Fri Aug 22 12:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8okr_16930/08_2025/8okr_16930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8okr_16930/08_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_16930/08_2025/8okr_16930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8okr_16930/08_2025/8okr_16930.map" model { file = "/net/cci-nas-00/data/ceres_data/8okr_16930/08_2025/8okr_16930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8okr_16930/08_2025/8okr_16930.cif" } resolution = 2.86 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= 0.001 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.50, per 1000 atoms: 0.31 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: 0.10 Conformation dependent library (CDL) restraints added in 33.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.04 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: 0.13 Time building geometry restraints manager: 0.15 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: 1.530 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.740 Find NCS groups from input model: 0.020 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:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.850 ------------------------------------------------------------------------------- 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= 0.486 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 1656) covalent geometry : angle 1.55752 ( 2136) hydrogen bonds : bond 0.03345 ( 18) hydrogen bonds : angle 7.97021 ( 54) *********************** 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 : 0.072 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: 1.1665 time to fit residues: 9.5030 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 : 0.069 ------------------------------------------------------------------------------- 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 = 0.055436 restraints weight = 3417.969| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.74 r_work: 0.2830 rms_B_bonded: 2.70 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= 8.584 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 : 138.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.18742 ( 1656) covalent geometry : angle 6.36491 ( 2136) hydrogen bonds : bond 0.43442 ( 18) hydrogen bonds : angle 11.89861 ( 54) *********************** 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 : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7820 (tppp) REVERT: R 2 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7826 (tppp) REVERT: H 2 LYS cc_start: 0.8679 (tttt) cc_final: 0.8175 (ttmp) REVERT: I 2 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8299 (mtpt) REVERT: I 4 LYS cc_start: 0.9162 (mttp) cc_final: 0.8776 (mttt) REVERT: K 2 LYS cc_start: 0.8679 (tttt) cc_final: 0.8176 (ttmp) REVERT: L 2 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8305 (mtpt) REVERT: L 4 LYS cc_start: 0.9162 (mttp) cc_final: 0.8777 (mttt) outliers start: 12 outliers final: 4 residues processed: 32 average time/residue: 0.9244 time to fit residues: 29.9260 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 : 0.073 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054696 restraints weight = 3602.814| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.79 r_work: 0.2822 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- 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= 8.716 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 : 147.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.18970 ( 1656) covalent geometry : angle 6.34889 ( 2136) hydrogen bonds : bond 0.45053 ( 18) hydrogen bonds : angle 11.94488 ( 54) *********************** 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 : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 6 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: U 7 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8252 (m-10) REVERT: X 6 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8736 (mt0) REVERT: X 7 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: O 2 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7878 (tppp) REVERT: O 6 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: R 2 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7874 (tppp) REVERT: R 6 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: H 2 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8415 (ttmp) REVERT: I 2 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8395 (mmtp) REVERT: I 4 LYS cc_start: 0.9291 (mttt) cc_final: 0.8902 (mttt) REVERT: K 2 LYS cc_start: 0.8750 (tttt) cc_final: 0.8362 (ttmp) REVERT: L 2 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8391 (mmtp) REVERT: L 4 LYS cc_start: 0.9288 (mttt) cc_final: 0.8898 (mttt) outliers start: 18 outliers final: 6 residues processed: 32 average time/residue: 0.8976 time to fit residues: 29.0574 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 : 0.075 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054112 restraints weight = 3488.752| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.95 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: 0.8977 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= 8.744 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 : 147.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19011 ( 1656) covalent geometry : angle 6.36978 ( 2136) hydrogen bonds : bond 0.45357 ( 18) hydrogen bonds : angle 11.92333 ( 54) *********************** 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 : 0.076 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: 0.8808 (mtpt) REVERT: X 6 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: X 7 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: O 2 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7785 (tppp) REVERT: R 2 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7783 (tppp) REVERT: H 2 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8401 (ttmp) REVERT: I 2 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8239 (mmtp) REVERT: I 4 LYS cc_start: 0.9280 (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: 0.8262 (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: 0.9356 time to fit residues: 35.9246 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 : 0.075 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.055070 restraints weight = 3688.768| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.04 r_work: 0.2819 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: 0.8927 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= 8.741 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 : 145.06 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19005 ( 1656) covalent geometry : angle 6.39197 ( 2136) hydrogen bonds : bond 0.45339 ( 18) hydrogen bonds : angle 11.93568 ( 54) *********************** 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 : 0.092 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: 0.8857 (mtpt) REVERT: U 7 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: W 4 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8894 (mtpt) REVERT: X 6 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: X 7 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: O 2 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7779 (tppp) REVERT: R 2 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7783 (tppp) REVERT: H 2 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8319 (ttmp) REVERT: I 2 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8261 (mmtp) REVERT: I 4 LYS cc_start: 0.9250 (mttp) cc_final: 0.8784 (mttt) REVERT: K 2 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8320 (ttmp) REVERT: L 2 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8292 (mmtp) REVERT: L 4 LYS cc_start: 0.9253 (mttp) cc_final: 0.8789 (mttt) REVERT: B 4 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8875 (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: 0.8909 (mtpt) REVERT: F 4 LYS cc_start: 0.9246 (mttp) cc_final: 0.8876 (mttp) outliers start: 26 outliers final: 9 residues processed: 35 average time/residue: 0.9369 time to fit residues: 33.1413 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 : 0.074 ------------------------------------------------------------------------------- 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 = 0.2966 r_free = 0.2966 target = 0.054648 restraints weight = 3520.105| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.83 r_work: 0.2829 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 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= 8.754 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 : 147.84 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19032 ( 1656) covalent geometry : angle 6.39434 ( 2136) hydrogen bonds : bond 0.45344 ( 18) hydrogen bonds : angle 11.94847 ( 54) *********************** 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 : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8839 (mtpt) REVERT: W 4 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8838 (mtpt) REVERT: X 6 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: O 2 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7920 (tppp) REVERT: R 2 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7927 (tppp) REVERT: I 2 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8337 (mmtp) REVERT: I 4 LYS cc_start: 0.9290 (mttp) cc_final: 0.8834 (mttt) REVERT: L 2 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8340 (mmtp) REVERT: L 4 LYS cc_start: 0.9295 (mttp) cc_final: 0.8846 (mttt) REVERT: B 4 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8840 (mtpt) REVERT: C 4 LYS cc_start: 0.9277 (mttp) cc_final: 0.8919 (mttp) REVERT: E 4 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8907 (mtpt) REVERT: F 4 LYS cc_start: 0.9278 (mttp) cc_final: 0.8926 (mttp) outliers start: 22 outliers final: 9 residues processed: 30 average time/residue: 0.9454 time to fit residues: 28.6676 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 : 0.053 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054625 restraints weight = 3533.697| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.80 r_work: 0.2826 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 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= 8.760 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 : 148.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19046 ( 1656) covalent geometry : angle 6.40548 ( 2136) hydrogen bonds : bond 0.45342 ( 18) hydrogen bonds : angle 11.93097 ( 54) *********************** 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 : 0.070 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: 0.8894 (mtpt) REVERT: W 4 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8896 (mtpt) REVERT: O 2 LYS cc_start: 0.8205 (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: 0.8579 (OUTLIER) cc_final: 0.8359 (mmtp) REVERT: I 4 LYS cc_start: 0.9297 (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: 0.8877 (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: 0.8905 time to fit residues: 27.0383 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 : 0.081 ------------------------------------------------------------------------------- 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 = 0.2961 r_free = 0.2961 target = 0.054415 restraints weight = 3602.635| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.86 r_work: 0.2824 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 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= 8.756 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 : 148.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19035 ( 1656) covalent geometry : angle 6.41207 ( 2136) hydrogen bonds : bond 0.45383 ( 18) hydrogen bonds : angle 11.95402 ( 54) *********************** 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 : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8883 (mtpt) REVERT: W 4 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8881 (mtpt) REVERT: X 6 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8511 (mt0) REVERT: O 2 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7920 (tppp) REVERT: R 2 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7932 (tppp) REVERT: I 2 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8338 (mmtp) REVERT: I 4 LYS cc_start: 0.9294 (mttp) cc_final: 0.8838 (mttt) REVERT: L 2 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8345 (mmtp) REVERT: L 4 LYS cc_start: 0.9298 (mttp) cc_final: 0.8850 (mttt) REVERT: B 4 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8840 (mtpt) REVERT: C 4 LYS cc_start: 0.9295 (mttp) cc_final: 0.8930 (mttp) REVERT: E 4 LYS cc_start: 0.9258 (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: 0.8970 time to fit residues: 25.4132 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 : 0.074 ------------------------------------------------------------------------------- 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 = 0.054466 restraints weight = 3550.255| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.83 r_work: 0.2825 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- 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= 8.757 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 : 148.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19037 ( 1656) covalent geometry : angle 6.41260 ( 2136) hydrogen bonds : bond 0.45383 ( 18) hydrogen bonds : angle 11.95129 ( 54) *********************** 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 : 0.077 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: 0.8881 (mtpt) REVERT: X 6 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8514 (mt0) REVERT: O 2 LYS cc_start: 0.8183 (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: 0.8336 (mmtp) REVERT: I 4 LYS cc_start: 0.9291 (mttp) cc_final: 0.8833 (mttt) REVERT: L 2 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (mmtp) REVERT: L 4 LYS cc_start: 0.9297 (mttp) cc_final: 0.8849 (mttt) REVERT: B 4 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8865 (mtpt) REVERT: C 4 LYS cc_start: 0.9281 (mttp) cc_final: 0.8915 (mttp) REVERT: E 4 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8906 (mtpt) REVERT: F 4 LYS cc_start: 0.9293 (mttp) cc_final: 0.8937 (mttp) outliers start: 20 outliers final: 11 residues processed: 28 average time/residue: 0.9127 time to fit residues: 25.8489 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 : 0.078 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054452 restraints weight = 3554.297| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.84 r_work: 0.2825 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 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= 8.757 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 : 149.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19037 ( 1656) covalent geometry : angle 6.41224 ( 2136) hydrogen bonds : bond 0.45388 ( 18) hydrogen bonds : angle 11.95182 ( 54) ********************** 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 : 0.057 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: 0.8883 (mtpt) REVERT: W 4 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8881 (mtpt) REVERT: X 6 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: O 2 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7917 (tppp) REVERT: R 2 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7927 (tppp) REVERT: I 2 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8335 (mmtp) REVERT: I 4 LYS cc_start: 0.9290 (mttp) cc_final: 0.8833 (mttt) REVERT: L 2 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8341 (mmtp) REVERT: L 4 LYS cc_start: 0.9295 (mttp) cc_final: 0.8846 (mttt) REVERT: B 4 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8839 (mtpt) REVERT: C 4 LYS cc_start: 0.9280 (mttp) cc_final: 0.8913 (mttp) REVERT: E 4 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8912 (mtpt) REVERT: F 4 LYS cc_start: 0.9293 (mttp) cc_final: 0.8937 (mttp) outliers start: 20 outliers final: 11 residues processed: 28 average time/residue: 0.8609 time to fit residues: 24.3666 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 : 0.079 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.054497 restraints weight = 3520.531| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.82 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: 0.8981 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= 8.757 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 : 149.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.19035 ( 1656) covalent geometry : angle 6.41248 ( 2136) hydrogen bonds : bond 0.45378 ( 18) hydrogen bonds : angle 11.95275 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 705.84 seconds wall clock time: 13 minutes 32.06 seconds (812.06 seconds total)