Starting phenix.real_space_refine on Sun Mar 10 14:51:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz9_34393/03_2024/8gz9_34393.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz9_34393/03_2024/8gz9_34393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz9_34393/03_2024/8gz9_34393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz9_34393/03_2024/8gz9_34393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz9_34393/03_2024/8gz9_34393.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz9_34393/03_2024/8gz9_34393.pdb" } resolution = 2.62 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= 0.001 sd= 0.004 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 34 5.16 5 C 1588 2.51 5 N 390 2.21 5 O 414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2426 Number of models: 1 Model: "" Number of chains: 58 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "N" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "d" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "O" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "G" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "W" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "e" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "H" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "X" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "f" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "Q" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "Y" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "g" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "R" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "J" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "Z" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "S" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "K" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "a" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "i" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "T" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "b" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "j" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "U" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "M" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "c" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "k" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.52, per 1000 atoms: 0.63 Number of scatterers: 2426 At special positions: 0 Unit cell: (135.29, 141.1, 34.86, 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 34 16.00 O 414 8.00 N 390 7.00 C 1588 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: 0.76 Conformation dependent library (CDL) restraints added in 448.5 milliseconds 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 722 1.33 - 1.45: 138 1.45 - 1.57: 1468 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 2396 Sorted by residual: bond pdb=" N VAL H 10 " pdb=" CA VAL H 10 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.83e+00 bond pdb=" N GLY H 7 " pdb=" CA GLY H 7 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.04e-02 9.25e+03 7.26e+00 bond pdb=" N LEU H 6 " pdb=" CA LEU H 6 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.01e+00 bond pdb=" N MET H 5 " pdb=" CA MET H 5 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.23e-02 6.61e+03 6.93e+00 bond pdb=" N GLY H 4 " pdb=" CA GLY H 4 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.23e-02 6.61e+03 6.74e+00 ... (remaining 2391 not shown) Histogram of bond angle deviations from ideal: 100.58 - 106.23: 143 106.23 - 111.87: 1229 111.87 - 117.52: 650 117.52 - 123.17: 981 123.17 - 128.82: 195 Bond angle restraints: 3198 Sorted by residual: angle pdb=" CA GLY H 7 " pdb=" C GLY H 7 " pdb=" O GLY H 7 " ideal model delta sigma weight residual 121.96 118.25 3.71 1.02e+00 9.61e-01 1.32e+01 angle pdb=" O GLY H 8 " pdb=" C GLY H 8 " pdb=" N VAL H 9 " ideal model delta sigma weight residual 122.18 124.71 -2.53 9.60e-01 1.09e+00 6.94e+00 angle pdb=" CA GLY c 8 " pdb=" C GLY c 8 " pdb=" N VAL c 9 " ideal model delta sigma weight residual 114.58 116.84 -2.26 8.60e-01 1.35e+00 6.92e+00 angle pdb=" CA GLY H 4 " pdb=" C GLY H 4 " pdb=" O GLY H 4 " ideal model delta sigma weight residual 121.55 118.38 3.17 1.22e+00 6.72e-01 6.75e+00 angle pdb=" CA LEU H 6 " pdb=" C LEU H 6 " pdb=" O LEU H 6 " ideal model delta sigma weight residual 121.11 118.22 2.89 1.17e+00 7.31e-01 6.09e+00 ... (remaining 3193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.65: 1106 11.65 - 23.31: 117 23.31 - 34.96: 67 34.96 - 46.62: 24 46.62 - 58.27: 8 Dihedral angle restraints: 1322 sinusoidal: 446 harmonic: 876 Sorted by residual: dihedral pdb=" CB MET V 5 " pdb=" CG MET V 5 " pdb=" SD MET V 5 " pdb=" CE MET V 5 " ideal model delta sinusoidal sigma weight residual 60.00 118.27 -58.27 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET i 5 " pdb=" CG MET i 5 " pdb=" SD MET i 5 " pdb=" CE MET i 5 " ideal model delta sinusoidal sigma weight residual -60.00 -117.28 57.28 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CB MET a 5 " pdb=" CG MET a 5 " pdb=" SD MET a 5 " pdb=" CE MET a 5 " ideal model delta sinusoidal sigma weight residual 180.00 124.69 55.31 3 1.50e+01 4.44e-03 9.34e+00 ... (remaining 1319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 266 0.037 - 0.075: 47 0.075 - 0.112: 86 0.112 - 0.149: 20 0.149 - 0.187: 5 Chirality restraints: 424 Sorted by residual: chirality pdb=" CA ILE H 11 " pdb=" N ILE H 11 " pdb=" C ILE H 11 " pdb=" CB ILE H 11 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA LEU H 6 " pdb=" N LEU H 6 " pdb=" C LEU H 6 " pdb=" CB LEU H 6 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA VAL H 9 " pdb=" N VAL H 9 " pdb=" C VAL H 9 " pdb=" CB VAL H 9 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 421 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Q 1 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.19e-01 pdb=" N PRO Q 2 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO Q 2 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO Q 2 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET k 5 " -0.004 2.00e-02 2.50e+03 8.77e-03 7.69e-01 pdb=" C MET k 5 " 0.015 2.00e-02 2.50e+03 pdb=" O MET k 5 " -0.006 2.00e-02 2.50e+03 pdb=" N LEU k 6 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY a 1 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.57e-01 pdb=" N PRO a 2 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO a 2 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO a 2 " -0.012 5.00e-02 4.00e+02 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.12: 1327 3.12 - 3.56: 1779 3.56 - 4.01: 2496 4.01 - 4.45: 2173 4.45 - 4.90: 4131 Nonbonded interactions: 11906 Sorted by model distance: nonbonded pdb=" O ALA H 12 " pdb=" CB ALA H 12 " model vdw 2.670 2.768 nonbonded pdb=" N GLY X 8 " pdb=" O GLY X 8 " model vdw 2.688 2.496 nonbonded pdb=" N GLY F 7 " pdb=" O GLY F 7 " model vdw 2.688 2.496 nonbonded pdb=" N GLY C 8 " pdb=" O GLY C 8 " model vdw 2.690 2.496 nonbonded pdb=" N GLY Z 8 " pdb=" O GLY Z 8 " model vdw 2.691 2.496 ... (remaining 11901 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 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'T' selection = chain 'Z' selection = chain 'e' selection = chain 'k' } 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: 1.870 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: 9.070 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.540 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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 : 0.003 0.035 2396 Z= 0.242 Angle : 0.686 8.054 3198 Z= 0.356 Chirality : 0.060 0.187 424 Planarity : 0.004 0.023 384 Dihedral : 14.014 58.271 802 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 23.89 % Favored : 76.11 % 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: -0.15 (0.46), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.10 (0.35), residues: 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.267 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.8359 time to fit residues: 48.1349 Evaluate side-chains 47 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2396 Z= 0.166 Angle : 0.630 5.298 3198 Z= 0.251 Chirality : 0.058 0.125 424 Planarity : 0.004 0.017 384 Dihedral : 3.300 10.827 356 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 5.31 % Allowed : 17.26 % Favored : 77.43 % 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: -0.24 (0.44), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.288 Fit side-chains REVERT: W 9 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8750 (t) REVERT: e 5 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8021 (mpp) outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 0.8596 time to fit residues: 47.7373 Evaluate side-chains 52 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain e residue 5 MET Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain c residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 0.0670 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 0.0050 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 overall best weight: 2.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2396 Z= 0.094 Angle : 0.524 4.799 3198 Z= 0.202 Chirality : 0.056 0.119 424 Planarity : 0.003 0.014 384 Dihedral : 2.863 9.388 356 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.54 % Allowed : 17.26 % Favored : 79.20 % 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: -0.15 (0.44), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.10 (0.34), residues: 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.267 Fit side-chains REVERT: N 9 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8867 (t) REVERT: W 9 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8749 (t) REVERT: e 5 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8027 (mpp) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.9299 time to fit residues: 48.6987 Evaluate side-chains 52 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain e residue 5 MET Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain U residue 3 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.0270 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2396 Z= 0.179 Angle : 0.619 4.847 3198 Z= 0.252 Chirality : 0.057 0.124 424 Planarity : 0.003 0.014 384 Dihedral : 3.586 11.117 356 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 5.31 % Allowed : 14.16 % Favored : 80.53 % 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: -0.29 (0.43), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.297 Fit side-chains REVERT: e 5 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8018 (mpp) outliers start: 12 outliers final: 5 residues processed: 52 average time/residue: 1.0162 time to fit residues: 54.3012 Evaluate side-chains 50 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain e residue 5 MET Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain c residue 9 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 overall best weight: 2.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2396 Z= 0.115 Angle : 0.543 4.572 3198 Z= 0.214 Chirality : 0.056 0.120 424 Planarity : 0.002 0.013 384 Dihedral : 3.221 10.343 356 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.54 % Allowed : 16.37 % Favored : 80.09 % 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: -0.26 (0.43), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.19 (0.33), residues: 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.270 Fit side-chains REVERT: W 9 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8723 (t) REVERT: e 5 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7990 (mpp) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.9167 time to fit residues: 48.0251 Evaluate side-chains 52 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain e residue 5 MET Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain c residue 9 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 0.0060 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2396 Z= 0.115 Angle : 0.533 4.492 3198 Z= 0.211 Chirality : 0.056 0.120 424 Planarity : 0.002 0.013 384 Dihedral : 3.221 10.285 356 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.98 % Allowed : 16.81 % Favored : 79.20 % 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: -0.21 (0.44), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.15 (0.33), residues: 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.271 Fit side-chains REVERT: W 9 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8730 (t) REVERT: e 5 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8047 (mpp) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.8935 time to fit residues: 47.7335 Evaluate side-chains 52 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain e residue 5 MET Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain c residue 9 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 23 optimal weight: 0.0570 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2396 Z= 0.107 Angle : 0.518 4.548 3198 Z= 0.205 Chirality : 0.056 0.119 424 Planarity : 0.002 0.012 384 Dihedral : 3.157 10.187 356 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 5.31 % Allowed : 15.49 % Favored : 79.20 % 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: -0.15 (0.44), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.10 (0.33), residues: 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.270 Fit side-chains REVERT: N 9 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8881 (t) REVERT: W 9 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8732 (t) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.9043 time to fit residues: 48.2992 Evaluate side-chains 51 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain c residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2396 Z= 0.213 Angle : 0.652 4.758 3198 Z= 0.271 Chirality : 0.058 0.126 424 Planarity : 0.003 0.015 384 Dihedral : 3.949 11.559 356 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.98 % Allowed : 15.93 % Favored : 80.09 % 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: -0.47 (0.43), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.35 (0.33), residues: 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.258 Fit side-chains REVERT: k 6 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8532 (tt) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.8891 time to fit residues: 50.2346 Evaluate side-chains 55 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain k residue 6 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.0030 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2396 Z= 0.084 Angle : 0.502 4.736 3198 Z= 0.196 Chirality : 0.056 0.124 424 Planarity : 0.002 0.013 384 Dihedral : 3.016 9.203 356 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.54 % Allowed : 17.26 % Favored : 79.20 % 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: -0.29 (0.43), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.273 Fit side-chains REVERT: N 9 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8874 (t) REVERT: W 9 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8703 (t) REVERT: k 6 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8483 (tt) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.8626 time to fit residues: 47.0022 Evaluate side-chains 53 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain k residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2396 Z= 0.118 Angle : 0.544 4.741 3198 Z= 0.216 Chirality : 0.056 0.125 424 Planarity : 0.002 0.012 384 Dihedral : 3.310 10.223 356 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.10 % Allowed : 17.26 % Favored : 79.65 % 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: -0.22 (0.44), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.15 (0.33), residues: 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 644 Ramachandran restraints generated. 322 Oldfield, 0 Emsley, 322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.266 Fit side-chains REVERT: W 9 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8721 (t) REVERT: k 6 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8521 (tt) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.9802 time to fit residues: 52.3161 Evaluate side-chains 53 residues out of total 226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain k residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 0.0570 chunk 9 optimal weight: 7.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136980 restraints weight = 2238.505| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.49 r_work: 0.3689 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2396 Z= 0.068 Angle : 0.478 4.572 3198 Z= 0.184 Chirality : 0.056 0.122 424 Planarity : 0.002 0.013 384 Dihedral : 2.712 8.473 356 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.10 % Allowed : 17.70 % Favored : 79.20 % 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: -0.04 (0.44), residues: 322 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.02 (0.34), residues: 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.18 seconds wall clock time: 25 minutes 53.51 seconds (1553.51 seconds total)