Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/09_2024/8okr_16930.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/09_2024/8okr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/09_2024/8okr_16930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/09_2024/8okr_16930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/09_2024/8okr_16930.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/09_2024/8okr_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-5461/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: 1.34, per 1000 atoms: 0.83 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: 1.01 Conformation dependent library (CDL) restraints added in 143.0 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: 0.34 Time building geometry restraints manager: 1.02 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.740 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.204 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: 2.0928 time to fit residues: 17.1839 Evaluate side-chains 2 residues out of total 168 non-(ALA, GLY, PRO) need fitting. 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7551 (tttt) REVERT: F 2 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7556 (tttt) outliers start: 12 outliers final: 4 residues processed: 32 average time/residue: 1.8324 time to fit residues: 59.4625 Evaluate side-chains 28 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain F residue 2 LYS 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 ** O 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 1.0424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.189 0.552 1656 Z=10.848 Angle : 6.392 32.613 2136 Z= 3.475 Chirality : 0.433 0.791 168 Planarity : 0.038 0.088 264 Dihedral : 29.849 82.114 168 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 152.86 Ramachandran Plot: Outliers : 11.67 % Allowed : 43.33 % Favored : 45.00 % Rotamer: Outliers : 10.71 % Allowed : 28.57 % Favored : 60.71 % 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 0.111 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 38 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 20 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 6 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: U 7 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: X 6 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: X 7 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7458 (m-10) REVERT: O 6 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: R 6 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8093 (mt0) outliers start: 18 outliers final: 6 residues processed: 28 average time/residue: 1.8101 time to fit residues: 51.4229 Evaluate side-chains 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 18 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 4 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 1.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.556 1656 Z=10.865 Angle : 6.412 33.474 2136 Z= 3.486 Chirality : 0.435 0.782 168 Planarity : 0.038 0.087 264 Dihedral : 30.290 90.000 168 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 154.42 Ramachandran Plot: Outliers : 10.83 % Allowed : 45.00 % Favored : 44.17 % Rotamer: Outliers : 14.29 % Allowed : 25.00 % 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: -7.75 (0.45), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.34), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.092 0.020 PHE U 7 *********************** 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 40 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 16 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8792 (mtpt) REVERT: U 7 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: W 4 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8797 (mtpt) REVERT: X 6 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: X 7 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: H 2 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7612 (ttmm) REVERT: K 2 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7623 (ttmm) REVERT: B 4 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8658 (mtpt) REVERT: E 4 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8651 (mtpt) outliers start: 24 outliers final: 9 residues processed: 32 average time/residue: 1.8491 time to fit residues: 59.9352 Evaluate side-chains 34 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 16 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 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 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 4 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 1.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.558 1656 Z=10.872 Angle : 6.447 33.641 2136 Z= 3.500 Chirality : 0.432 0.781 168 Planarity : 0.038 0.087 264 Dihedral : 30.441 87.325 168 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 152.91 Ramachandran Plot: Outliers : 9.17 % Allowed : 49.17 % Favored : 41.67 % Rotamer: Outliers : 14.29 % Allowed : 25.60 % Favored : 60.12 % 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 : -5.89 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.090 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 40 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 16 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8845 (mtpt) REVERT: W 4 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8838 (mtpt) REVERT: X 6 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: X 7 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: H 2 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7609 (ttmm) REVERT: K 2 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7615 (ttmm) REVERT: B 4 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8693 (mtpt) REVERT: E 4 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8689 (mtpt) outliers start: 24 outliers final: 9 residues processed: 31 average time/residue: 1.7275 time to fit residues: 54.2890 Evaluate side-chains 33 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 16 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 X residue 7 PHE Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 4 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: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 1.0688 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=10.884 Angle : 6.479 35.266 2136 Z= 3.508 Chirality : 0.432 0.777 168 Planarity : 0.038 0.087 264 Dihedral : 30.667 89.104 168 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 152.16 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 10.12 % Allowed : 29.17 % 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: -7.74 (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 0.086 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 31 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 14 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8836 (mtpt) REVERT: W 4 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8841 (mtpt) REVERT: X 6 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: H 2 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7608 (ttmm) REVERT: K 2 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7622 (ttmm) REVERT: B 4 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8694 (mtpt) REVERT: E 4 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8657 (mtpt) outliers start: 17 outliers final: 9 residues processed: 25 average time/residue: 1.9295 time to fit residues: 48.8803 Evaluate side-chains 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 4 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: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 1.0722 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=10.884 Angle : 6.499 34.425 2136 Z= 3.513 Chirality : 0.433 0.779 168 Planarity : 0.038 0.087 264 Dihedral : 30.703 88.030 168 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 154.26 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 11.90 % Allowed : 29.17 % Favored : 58.93 % 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: -7.72 (0.48), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.36), 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 34 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 14 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8845 (mtpt) REVERT: W 4 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8846 (mtpt) REVERT: H 2 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7608 (ttmm) REVERT: K 2 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7624 (ttmm) REVERT: B 4 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8700 (mtpt) REVERT: E 4 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8659 (mtpt) outliers start: 20 outliers final: 10 residues processed: 28 average time/residue: 1.7278 time to fit residues: 49.0952 Evaluate side-chains 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 4 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 1.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.558 1656 Z=10.890 Angle : 6.490 33.957 2136 Z= 3.511 Chirality : 0.434 0.788 168 Planarity : 0.038 0.087 264 Dihedral : 30.711 88.840 168 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 156.45 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 11.90 % Allowed : 29.17 % Favored : 58.93 % 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 : -5.89 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.020 PHE M 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 34 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 14 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8848 (mtpt) REVERT: W 4 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8847 (mtpt) REVERT: H 2 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7610 (ttmm) REVERT: K 2 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7625 (ttmm) REVERT: B 4 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8699 (mtpt) REVERT: E 4 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8658 (mtpt) outliers start: 20 outliers final: 10 residues processed: 28 average time/residue: 1.8561 time to fit residues: 52.6638 Evaluate side-chains 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 4 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 1.0768 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=10.894 Angle : 6.498 33.668 2136 Z= 3.513 Chirality : 0.434 0.789 168 Planarity : 0.038 0.087 264 Dihedral : 30.745 88.930 168 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 155.82 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 9.52 % Allowed : 30.95 % Favored : 59.52 % 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 0.086 0.020 PHE M 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 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8847 (mtpt) REVERT: W 4 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8846 (mtpt) REVERT: H 2 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7609 (ttmm) REVERT: K 2 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7625 (ttmm) REVERT: B 4 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8699 (mtpt) REVERT: E 4 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8659 (mtpt) outliers start: 16 outliers final: 10 residues processed: 24 average time/residue: 1.9482 time to fit residues: 47.4572 Evaluate side-chains 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 4 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 1.0778 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=10.891 Angle : 6.519 33.576 2136 Z= 3.523 Chirality : 0.434 0.780 168 Planarity : 0.038 0.087 264 Dihedral : 30.774 89.125 168 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 155.19 Ramachandran Plot: Outliers : 11.67 % Allowed : 46.67 % Favored : 41.67 % Rotamer: Outliers : 9.52 % Allowed : 30.95 % Favored : 59.52 % 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: -7.71 (0.47), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.87 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.020 PHE M 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 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8847 (mtpt) REVERT: W 4 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8846 (mtpt) REVERT: H 2 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7609 (ttmm) REVERT: K 2 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7626 (ttmm) REVERT: B 4 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8699 (mtpt) REVERT: E 4 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8690 (mtpt) outliers start: 16 outliers final: 10 residues processed: 24 average time/residue: 1.9752 time to fit residues: 48.0845 Evaluate side-chains 30 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 6 GLN Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 4 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 = 0.3492 r_free = 0.3492 target = 0.083321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.055212 restraints weight = 3742.744| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.91 r_work: 0.2850 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 1.0787 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=10.892 Angle : 6.503 33.496 2136 Z= 3.517 Chirality : 0.434 0.780 168 Planarity : 0.038 0.087 264 Dihedral : 30.777 89.258 168 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 155.51 Ramachandran Plot: Outliers : 10.00 % Allowed : 48.33 % Favored : 41.67 % Rotamer: Outliers : 9.52 % Allowed : 30.95 % Favored : 59.52 % 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: -7.72 (0.47), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 0.020 PHE M 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 819.45 seconds wall clock time: 15 minutes 14.80 seconds (914.80 seconds total)