Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/03_2024/8okr_16930.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/03_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_16930/03_2024/8okr_16930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/03_2024/8okr_16930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/03_2024/8okr_16930.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okr_16930/03_2024/8okr_16930.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 0.98, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 0.55 Conformation dependent library (CDL) restraints added in 181.9 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: 0.18 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: 0.29 Time building geometry restraints manager: 0.61 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: 100.53 - 106.02: 58 106.02 - 111.51: 454 111.51 - 116.99: 464 116.99 - 122.48: 994 122.48 - 127.97: 166 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 2.520 nonbonded pdb=" NZ LYS N 4 " pdb=" O PHE G 7 " model vdw 1.489 2.520 nonbonded pdb=" NZ LYS T 4 " pdb=" O PHE M 7 " model vdw 1.490 2.520 nonbonded pdb=" NZ LYS W 4 " pdb=" O PHE P 7 " model vdw 1.490 2.520 nonbonded pdb=" NZ LYS H 4 " pdb=" O PHE A 7 " model vdw 1.490 2.520 ... (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 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: 1.150 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: 5.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.400 Find NCS groups from input model: 0.110 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- 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: 2.0902 time to fit residues: 17.1611 Evaluate side-chains 2 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.9546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.187 0.551 1656 Z=10.708 Angle : 6.354 33.111 2136 Z= 3.399 Chirality : 0.432 0.839 168 Planarity : 0.039 0.097 264 Dihedral : 25.555 75.822 168 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 143.21 Ramachandran Plot: Outliers : 23.33 % Allowed : 21.67 % Favored : 55.00 % Rotamer: Outliers : 9.52 % Allowed : 19.05 % Favored : 71.43 % Cbeta Deviations : 31.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.56 % 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: -7.70 (0.37), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.86 (0.28), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.106 0.021 PHE H 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 46 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 2 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7436 (ttmm) REVERT: Q 2 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7416 (ttmm) outliers start: 16 outliers final: 4 residues processed: 36 average time/residue: 1.6817 time to fit residues: 61.3419 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 N residue 2 LYS Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain I residue 6 GLN 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: ** 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: 1.0339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.188 0.554 1656 Z=10.776 Angle : 6.452 35.011 2136 Z= 3.484 Chirality : 0.430 0.788 168 Planarity : 0.039 0.088 264 Dihedral : 28.432 81.278 168 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 158.59 Ramachandran Plot: Outliers : 13.33 % Allowed : 42.50 % Favored : 44.17 % Rotamer: Outliers : 13.10 % Allowed : 22.62 % Favored : 64.29 % Cbeta Deviations : 33.93 % 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: -7.69 (0.45), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.86 (0.34), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 0.021 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 40 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 18 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 6 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: U 7 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: X 6 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: X 7 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7393 (m-10) outliers start: 22 outliers final: 12 residues processed: 34 average time/residue: 1.6977 time to fit residues: 58.5099 Evaluate side-chains 34 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain Q residue 2 LYS 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 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: ** 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: 0.8237 moved from start: 1.0436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.189 0.554 1656 Z=10.801 Angle : 6.475 35.195 2136 Z= 3.497 Chirality : 0.429 0.783 168 Planarity : 0.038 0.087 264 Dihedral : 28.983 81.887 168 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 163.02 Ramachandran Plot: Outliers : 13.33 % Allowed : 45.00 % Favored : 41.67 % Rotamer: Outliers : 17.86 % Allowed : 20.83 % Favored : 61.31 % Cbeta Deviations : 34.52 % 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 (0.46), 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 0.084 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 49 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 19 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8695 (mtpt) REVERT: U 7 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: W 4 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8722 (mtpt) REVERT: X 7 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: B 4 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: E 4 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8687 (mtpt) outliers start: 30 outliers final: 16 residues processed: 39 average time/residue: 1.7642 time to fit residues: 69.6296 Evaluate side-chains 37 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 15 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 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 N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 PHE 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: ** 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: 0.8241 moved from start: 1.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.189 0.556 1656 Z=10.814 Angle : 6.487 35.158 2136 Z= 3.510 Chirality : 0.429 0.783 168 Planarity : 0.038 0.087 264 Dihedral : 29.455 84.938 168 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 163.07 Ramachandran Plot: Outliers : 11.67 % Allowed : 48.33 % Favored : 40.00 % Rotamer: Outliers : 18.45 % Allowed : 20.83 % Favored : 60.71 % Cbeta Deviations : 34.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.77 (0.47), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.92 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.087 0.020 PHE U 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 50 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 19 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 2 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7758 (ttmm) REVERT: T 4 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8738 (mtpt) REVERT: U 7 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7737 (m-10) REVERT: W 4 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8767 (mtpt) REVERT: X 7 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: B 4 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8716 (mtpt) REVERT: E 4 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8718 (mtpt) outliers start: 31 outliers final: 18 residues processed: 40 average time/residue: 1.6238 time to fit residues: 65.8096 Evaluate side-chains 39 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 14 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 2 LYS Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 1 CYS 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 1 CYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 7 PHE Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 PHE 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: ** 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: 0.8245 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 : 0.189 0.558 1656 Z=10.834 Angle : 6.480 35.105 2136 Z= 3.506 Chirality : 0.429 0.780 168 Planarity : 0.038 0.087 264 Dihedral : 29.834 87.172 168 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 165.57 Ramachandran Plot: Outliers : 10.83 % Allowed : 49.17 % Favored : 40.00 % Rotamer: Outliers : 15.48 % Allowed : 25.00 % Favored : 59.52 % Cbeta Deviations : 34.52 % 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 (0.48), 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 U 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 14 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8739 (mtpt) REVERT: W 4 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8738 (mtpt) REVERT: B 4 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8722 (mtpt) REVERT: E 4 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8721 (mtpt) outliers start: 26 outliers final: 17 residues processed: 34 average time/residue: 1.6876 time to fit residues: 58.1481 Evaluate side-chains 31 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 10 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS 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: ** 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: 0.8244 moved from start: 1.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.189 0.559 1656 Z=10.840 Angle : 6.488 35.040 2136 Z= 3.510 Chirality : 0.429 0.781 168 Planarity : 0.038 0.086 264 Dihedral : 29.992 86.866 168 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 165.83 Ramachandran Plot: Outliers : 11.67 % Allowed : 49.17 % Favored : 39.17 % Rotamer: Outliers : 16.67 % Allowed : 25.00 % Favored : 58.33 % Cbeta Deviations : 34.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.72 % 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 P 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 42 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 14 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8739 (mtpt) REVERT: W 4 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8740 (mtpt) REVERT: B 4 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8720 (mtpt) REVERT: E 4 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8721 (mtpt) outliers start: 28 outliers final: 18 residues processed: 36 average time/residue: 1.7735 time to fit residues: 64.6658 Evaluate side-chains 36 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 14 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 1 CYS Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS 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: ** 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: 0.8245 moved from start: 1.0792 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=10.854 Angle : 6.480 34.378 2136 Z= 3.510 Chirality : 0.431 0.780 168 Planarity : 0.038 0.087 264 Dihedral : 30.213 87.542 168 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 167.71 Ramachandran Plot: Outliers : 11.67 % Allowed : 50.00 % Favored : 38.33 % Rotamer: Outliers : 13.10 % Allowed : 26.79 % Favored : 60.12 % Cbeta Deviations : 35.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.74 (0.47), residues: 120 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.90 (0.36), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.086 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 36 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 14 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8744 (mtpt) REVERT: W 4 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8739 (mtpt) REVERT: B 4 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8717 (mtpt) REVERT: E 4 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8719 (mtpt) outliers start: 22 outliers final: 17 residues processed: 30 average time/residue: 1.6820 time to fit residues: 51.1722 Evaluate side-chains 35 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 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 N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS 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: ** 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: 0.8246 moved from start: 1.0892 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=10.867 Angle : 6.454 33.472 2136 Z= 3.507 Chirality : 0.434 0.798 168 Planarity : 0.038 0.086 264 Dihedral : 30.711 87.284 168 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 169.27 Ramachandran Plot: Outliers : 11.67 % Allowed : 49.17 % Favored : 39.17 % Rotamer: Outliers : 15.48 % Allowed : 23.81 % Favored : 60.71 % Cbeta Deviations : 35.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.72 % 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 P 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 12 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8739 (mtpt) REVERT: W 4 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8735 (mtpt) REVERT: O 6 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: R 6 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: B 4 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8720 (mtpt) REVERT: E 4 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8717 (mtpt) outliers start: 26 outliers final: 18 residues processed: 32 average time/residue: 1.4323 time to fit residues: 46.5260 Evaluate side-chains 36 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 12 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 1 CYS Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS 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 1 CYS 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: ** 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: 0.8244 moved from start: 1.0913 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=10.878 Angle : 6.452 33.438 2136 Z= 3.503 Chirality : 0.434 0.783 168 Planarity : 0.038 0.087 264 Dihedral : 30.791 88.678 168 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 170.89 Ramachandran Plot: Outliers : 11.67 % Allowed : 50.00 % Favored : 38.33 % Rotamer: Outliers : 16.07 % Allowed : 23.21 % Favored : 60.71 % Cbeta Deviations : 35.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.72 % 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 P 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 11 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 4 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8737 (mtpt) REVERT: U 5 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.6998 (t80) REVERT: W 4 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8737 (mtpt) REVERT: O 6 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: R 6 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: B 4 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8716 (mtpt) REVERT: E 4 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8721 (mtpt) outliers start: 27 outliers final: 19 residues processed: 33 average time/residue: 1.4998 time to fit residues: 50.2591 Evaluate side-chains 37 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 11 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain U residue 5 PHE Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain W residue 4 LYS Chi-restraints excluded: chain X residue 1 CYS Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain Q residue 2 LYS Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain I residue 1 CYS 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 1 CYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain C residue 1 CYS 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: ** 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 = 0.084424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.055860 restraints weight = 3685.888| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.84 r_work: 0.2853 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 1.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.190 0.560 1656 Z=10.884 Angle : 6.453 33.453 2136 Z= 3.502 Chirality : 0.434 0.779 168 Planarity : 0.038 0.087 264 Dihedral : 30.883 89.530 168 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 169.69 Ramachandran Plot: Outliers : 11.67 % Allowed : 50.00 % Favored : 38.33 % Rotamer: Outliers : 14.29 % Allowed : 25.00 % Favored : 60.71 % Cbeta Deviations : 35.71 % 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 P 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 859.22 seconds wall clock time: 17 minutes 32.37 seconds (1052.37 seconds total)