Starting phenix.real_space_refine on Thu Oct 22 18:17:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9net_49335/10_2026/9net_49335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9net_49335/10_2026/9net_49335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9net_49335/10_2026/9net_49335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9net_49335/10_2026/9net_49335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9net_49335/10_2026/9net_49335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9net_49335/10_2026/9net_49335.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.029 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 P 52 5.49 5 C 2184 2.51 5 N 468 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3432 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {'UQ4': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="UQ4 A 1 " pdbres="LEU A 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UQ4:plan-4': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p Time building chain proxies: 0.43, per 1000 atoms: 0.13 Number of scatterers: 3432 At special positions: 0 Unit cell: (86.24, 86.24, 32.48, 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) P 52 15.00 O 728 8.00 N 468 7.00 C 2184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=52, symmetry=0 Number of additional bonds: simple=52, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 41.1 milliseconds 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 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: 0.33 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: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.27: 416 1.27 - 1.36: 416 1.36 - 1.46: 988 1.46 - 1.56: 1612 1.56 - 1.66: 52 Bond restraints: 3484 Sorted by residual: bond pdb=" C53 UQ4 a 1 " pdb=" N52 UQ4 a 1 " ideal model delta sigma weight residual 1.342 1.508 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" C53 UQ4 C 1 " pdb=" N52 UQ4 C 1 " ideal model delta sigma weight residual 1.342 1.507 -0.165 2.00e-02 2.50e+03 6.85e+01 bond pdb=" C53 UQ4 n 1 " pdb=" N52 UQ4 n 1 " ideal model delta sigma weight residual 1.342 1.507 -0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" C53 UQ4 6 1 " pdb=" N52 UQ4 6 1 " ideal model delta sigma weight residual 1.342 1.507 -0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" C53 UQ4 k 1 " pdb=" N52 UQ4 k 1 " ideal model delta sigma weight residual 1.342 1.507 -0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 3479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.51: 4416 7.51 - 15.03: 56 15.03 - 22.54: 104 22.54 - 30.05: 104 30.05 - 37.56: 104 Bond angle restraints: 4784 Sorted by residual: angle pdb=" O2P PTR 0 6 " pdb=" P PTR 0 6 " pdb=" O3P PTR 0 6 " ideal model delta sigma weight residual 116.26 78.70 37.56 3.00e+00 1.11e-01 1.57e+02 angle pdb=" O2P PTR g 6 " pdb=" P PTR g 6 " pdb=" O3P PTR g 6 " ideal model delta sigma weight residual 116.26 78.70 37.56 3.00e+00 1.11e-01 1.57e+02 angle pdb=" O2P PTR 5 6 " pdb=" P PTR 5 6 " pdb=" O3P PTR 5 6 " ideal model delta sigma weight residual 116.26 78.70 37.56 3.00e+00 1.11e-01 1.57e+02 angle pdb=" O2P PTR i 6 " pdb=" P PTR i 6 " pdb=" O3P PTR i 6 " ideal model delta sigma weight residual 116.26 78.70 37.56 3.00e+00 1.11e-01 1.57e+02 angle pdb=" O2P PTR M 6 " pdb=" P PTR M 6 " pdb=" O3P PTR M 6 " ideal model delta sigma weight residual 116.26 78.71 37.55 3.00e+00 1.11e-01 1.57e+02 ... (remaining 4779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 1080 14.39 - 28.78: 428 28.78 - 43.17: 364 43.17 - 57.56: 48 57.56 - 71.95: 56 Dihedral angle restraints: 1976 sinusoidal: 1248 harmonic: 728 Sorted by residual: dihedral pdb=" CA LEU 6 4 " pdb=" CB LEU 6 4 " pdb=" CG LEU 6 4 " pdb=" CD1 LEU 6 4 " ideal model delta sinusoidal sigma weight residual 180.00 141.67 38.33 3 1.50e+01 4.44e-03 6.74e+00 dihedral pdb=" CA LEU h 4 " pdb=" CB LEU h 4 " pdb=" CG LEU h 4 " pdb=" CD1 LEU h 4 " ideal model delta sinusoidal sigma weight residual 180.00 141.67 38.33 3 1.50e+01 4.44e-03 6.74e+00 dihedral pdb=" CA LEU B 4 " pdb=" CB LEU B 4 " pdb=" CG LEU B 4 " pdb=" CD1 LEU B 4 " ideal model delta sinusoidal sigma weight residual 180.00 141.67 38.33 3 1.50e+01 4.44e-03 6.74e+00 ... (remaining 1973 not shown) Histogram of chiral volume deviations from ideal: 0.014 - 0.047: 364 0.047 - 0.080: 52 0.080 - 0.114: 0 0.114 - 0.147: 0 0.147 - 0.180: 52 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA PTR c 6 " pdb=" N PTR c 6 " pdb=" C PTR c 6 " pdb=" CB PTR c 6 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA PTR 5 6 " pdb=" N PTR 5 6 " pdb=" C PTR 5 6 " pdb=" CB PTR 5 6 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA PTR b 6 " pdb=" N PTR b 6 " pdb=" C PTR b 6 " pdb=" CB PTR b 6 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 465 not shown) Planarity restraints: 416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PTR p 6 " -0.000 2.00e-02 2.50e+03 4.24e-03 3.59e-01 pdb=" CG PTR p 6 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 PTR p 6 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PTR p 6 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PTR p 6 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PTR p 6 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PTR p 6 " -0.010 2.00e-02 2.50e+03 pdb=" OH PTR p 6 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PTR o 6 " -0.001 2.00e-02 2.50e+03 4.22e-03 3.56e-01 pdb=" CG PTR o 6 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 PTR o 6 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PTR o 6 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PTR o 6 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PTR o 6 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PTR o 6 " -0.010 2.00e-02 2.50e+03 pdb=" OH PTR o 6 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PTR 1 6 " -0.001 2.00e-02 2.50e+03 4.22e-03 3.56e-01 pdb=" CG PTR 1 6 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 PTR 1 6 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PTR 1 6 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PTR 1 6 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PTR 1 6 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PTR 1 6 " -0.010 2.00e-02 2.50e+03 pdb=" OH PTR 1 6 " 0.005 2.00e-02 2.50e+03 ... (remaining 413 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1885 3.03 - 3.50: 4064 3.50 - 3.97: 5114 3.97 - 4.43: 7002 4.43 - 4.90: 9031 Nonbonded interactions: 27096 Sorted by model distance: nonbonded pdb=" C51 UQ4 i 1 " pdb=" O01 UQ4 i 1 " model vdw 2.568 2.752 nonbonded pdb=" C51 UQ4 a 1 " pdb=" O01 UQ4 a 1 " model vdw 2.568 2.752 nonbonded pdb=" C51 UQ4 H 1 " pdb=" O01 UQ4 H 1 " model vdw 2.568 2.752 nonbonded pdb=" CZ PTR X 6 " pdb=" O2P PTR X 6 " model vdw 2.568 2.608 nonbonded pdb=" C51 UQ4 U 1 " pdb=" O01 UQ4 U 1 " model vdw 2.568 2.752 ... (remaining 27091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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' selection = chain 'Y' selection = chain 'Z' selection = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = 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' } 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 group one per residue 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 : 0.044 0.166 3536 Z= 2.492 Angle : 7.429 37.565 4784 Z= 2.480 Chirality : 0.068 0.180 468 Planarity : 0.002 0.004 416 Dihedral : 28.297 71.949 1456 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 53.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.34 (0.04), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.11 (0.03), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.04285 / 2.14 ( 3484) covalent geometry : angle 7.42851 / 2.48 ( 4784) Misc. bond : bond 0.10717 / 5.87 ( 52) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.089 Fit side-chains REVERT: A 2 LEU cc_start: 0.8985 (pt) cc_final: 0.8757 (pp) REVERT: I 2 LEU cc_start: 0.8793 (pt) cc_final: 0.8528 (pp) REVERT: M 2 LEU cc_start: 0.8973 (pt) cc_final: 0.8720 (pp) REVERT: S 2 LEU cc_start: 0.9044 (pt) cc_final: 0.8773 (pp) REVERT: W 2 LEU cc_start: 0.9036 (pt) cc_final: 0.8720 (pp) REVERT: 0 2 LEU cc_start: 0.8937 (pt) cc_final: 0.8713 (pp) REVERT: 2 2 LEU cc_start: 0.8869 (pt) cc_final: 0.8584 (pp) REVERT: 3 2 LEU cc_start: 0.9059 (pt) cc_final: 0.8798 (pp) REVERT: f 2 LEU cc_start: 0.9202 (pt) cc_final: 0.8994 (pp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0291 time to fit residues: 6.3649 Evaluate side-chains 123 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.123479 restraints weight = 6199.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.127191 restraints weight = 3318.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.129760 restraints weight = 2189.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.131493 restraints weight = 1610.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.132563 restraints weight = 1290.086| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3536 Z= 0.105 Angle : 0.806 6.717 4784 Z= 0.283 Chirality : 0.052 0.135 468 Planarity : 0.001 0.003 416 Dihedral : 28.829 59.914 1040 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 16.35 % Allowed : 44.23 % Favored : 39.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.04 (0.14), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.12 (0.11), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 3484) covalent geometry : angle 0.80563 / 0.28 ( 4784) Misc. bond : bond 0.00025 / 0.01 ( 52) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.090 Fit side-chains REVERT: G 5 LEU cc_start: 0.8617 (mm) cc_final: 0.8375 (mp) REVERT: H 2 LEU cc_start: 0.9277 (pt) cc_final: 0.9076 (pt) REVERT: I 4 LEU cc_start: 0.8509 (tp) cc_final: 0.8222 (tp) REVERT: W 5 LEU cc_start: 0.8594 (mm) cc_final: 0.8332 (mp) REVERT: Z 2 LEU cc_start: 0.8983 (pp) cc_final: 0.8739 (pt) REVERT: 3 2 LEU cc_start: 0.9016 (pt) cc_final: 0.8747 (pp) REVERT: 3 4 LEU cc_start: 0.8052 (tt) cc_final: 0.7759 (tt) REVERT: d 2 LEU cc_start: 0.9325 (pp) cc_final: 0.9087 (pt) REVERT: e 2 LEU cc_start: 0.9000 (pp) cc_final: 0.8779 (pt) REVERT: l 5 LEU cc_start: 0.8625 (mm) cc_final: 0.8396 (mt) REVERT: o 4 LEU cc_start: 0.8085 (tt) cc_final: 0.7884 (tt) outliers start: 34 outliers final: 12 residues processed: 131 average time/residue: 0.0280 time to fit residues: 5.4114 Evaluate side-chains 129 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.135787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118424 restraints weight = 6482.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.122162 restraints weight = 3158.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.124528 restraints weight = 1967.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.126050 restraints weight = 1435.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127116 restraints weight = 1149.836| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.047 3536 Z= 0.718 Angle : 1.533 10.349 4784 Z= 0.553 Chirality : 0.065 0.142 468 Planarity : 0.003 0.008 416 Dihedral : 25.286 59.505 1040 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 13.46 % Allowed : 46.63 % Favored : 39.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.64 (0.22), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.58 (0.17), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01509 / 0.72 ( 3484) covalent geometry : angle 1.53268 / 0.55 ( 4784) Misc. bond : bond 0.00260 / 0.14 ( 52) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 LEU cc_start: 0.8512 (mp) cc_final: 0.8290 (mp) REVERT: I 4 LEU cc_start: 0.8511 (tp) cc_final: 0.8211 (tp) REVERT: 1 4 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8479 (tt) REVERT: 5 4 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8813 (tt) REVERT: 8 3 LEU cc_start: 0.8497 (mp) cc_final: 0.8160 (mp) REVERT: d 4 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8790 (tt) REVERT: i 4 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8176 (tt) REVERT: o 3 LEU cc_start: 0.8249 (mp) cc_final: 0.8026 (mp) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.0311 time to fit residues: 6.7426 Evaluate side-chains 166 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain W residue 2 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.142898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.124615 restraints weight = 6098.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128486 restraints weight = 3144.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.130899 restraints weight = 1991.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132516 restraints weight = 1451.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.133550 restraints weight = 1157.742| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 3536 Z= 0.097 Angle : 0.926 8.044 4784 Z= 0.306 Chirality : 0.052 0.132 468 Planarity : 0.001 0.004 416 Dihedral : 24.179 59.160 1040 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 10.10 % Allowed : 57.21 % Favored : 32.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.15 (0.24), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.20 (0.18), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 3484) covalent geometry : angle 0.92596 / 0.31 ( 4784) Misc. bond : bond 0.00026 / 0.01 ( 52) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.107 Fit side-chains REVERT: G 5 LEU cc_start: 0.8676 (mm) cc_final: 0.8461 (mp) REVERT: I 4 LEU cc_start: 0.8419 (tp) cc_final: 0.8137 (tp) REVERT: V 4 LEU cc_start: 0.8235 (tt) cc_final: 0.7955 (tt) REVERT: 9 4 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8481 (tt) REVERT: c 5 LEU cc_start: 0.8771 (mm) cc_final: 0.8529 (mp) REVERT: d 4 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8734 (tt) REVERT: h 3 LEU cc_start: 0.8256 (mp) cc_final: 0.8056 (mp) REVERT: i 4 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7936 (tt) REVERT: l 5 LEU cc_start: 0.8316 (mm) cc_final: 0.8086 (mt) outliers start: 21 outliers final: 8 residues processed: 144 average time/residue: 0.0267 time to fit residues: 5.6270 Evaluate side-chains 138 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain R residue 2 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 4 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.137497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.120259 restraints weight = 6387.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.124069 restraints weight = 3096.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126438 restraints weight = 1950.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.127785 restraints weight = 1426.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128864 restraints weight = 1164.467| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.051 3536 Z= 0.717 Angle : 1.598 10.418 4784 Z= 0.568 Chirality : 0.068 0.135 468 Planarity : 0.003 0.008 416 Dihedral : 24.450 59.802 1040 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 13.94 % Allowed : 50.96 % Favored : 35.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.47 (0.31), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.45 (0.23), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01499 / 0.72 ( 3484) covalent geometry : angle 1.59801 / 0.57 ( 4784) Misc. bond : bond 0.00228 / 0.12 ( 52) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 4 LEU cc_start: 0.8660 (tp) cc_final: 0.8370 (tp) REVERT: J 3 LEU cc_start: 0.8640 (mp) cc_final: 0.8364 (mp) REVERT: U 4 LEU cc_start: 0.8551 (tt) cc_final: 0.8292 (tp) REVERT: 5 4 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8849 (tt) REVERT: 8 3 LEU cc_start: 0.8517 (mp) cc_final: 0.8295 (mp) REVERT: m 4 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8270 (tt) outliers start: 29 outliers final: 22 residues processed: 156 average time/residue: 0.0285 time to fit residues: 6.5028 Evaluate side-chains 173 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain R residue 2 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain Z residue 2 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 9 residue 2 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.142268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.124497 restraints weight = 6250.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.128485 restraints weight = 3061.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.130968 restraints weight = 1918.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132503 restraints weight = 1394.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133624 restraints weight = 1123.328| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 3536 Z= 0.097 Angle : 0.951 9.000 4784 Z= 0.314 Chirality : 0.053 0.135 468 Planarity : 0.001 0.005 416 Dihedral : 24.093 59.993 1040 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 11.06 % Allowed : 53.37 % Favored : 35.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.28 (0.30), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.31 (0.23), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 3484) covalent geometry : angle 0.95145 / 0.31 ( 4784) Misc. bond : bond 0.00039 / 0.02 ( 52) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.096 Fit side-chains REVERT: B 4 LEU cc_start: 0.8541 (tp) cc_final: 0.8284 (tp) REVERT: I 4 LEU cc_start: 0.8600 (tp) cc_final: 0.8324 (tp) REVERT: 1 4 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (tt) REVERT: 8 3 LEU cc_start: 0.8515 (mp) cc_final: 0.8275 (mp) REVERT: d 4 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8680 (tt) REVERT: g 2 LEU cc_start: 0.9044 (pp) cc_final: 0.8794 (pt) REVERT: i 2 LEU cc_start: 0.8557 (pt) cc_final: 0.7349 (tp) REVERT: l 3 LEU cc_start: 0.8559 (mp) cc_final: 0.8324 (mp) REVERT: m 4 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8165 (tt) outliers start: 23 outliers final: 10 residues processed: 150 average time/residue: 0.0311 time to fit residues: 6.8092 Evaluate side-chains 151 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain R residue 2 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 9 residue 2 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131330 restraints weight = 6562.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.135483 restraints weight = 3058.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138038 restraints weight = 1873.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139665 restraints weight = 1333.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.140726 restraints weight = 1038.322| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.044 3536 Z= 0.714 Angle : 1.597 10.155 4784 Z= 0.570 Chirality : 0.069 0.172 468 Planarity : 0.003 0.008 416 Dihedral : 24.260 59.725 1040 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 15.87 % Allowed : 47.60 % Favored : 36.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.35 (0.37), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.36 (0.28), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01490 / 0.72 ( 3484) covalent geometry : angle 1.59711 / 0.57 ( 4784) Misc. bond : bond 0.00246 / 0.13 ( 52) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8805 (tp) cc_final: 0.8594 (tp) REVERT: G 5 LEU cc_start: 0.8837 (mm) cc_final: 0.8611 (mp) REVERT: I 4 LEU cc_start: 0.8836 (tp) cc_final: 0.8534 (tp) REVERT: J 3 LEU cc_start: 0.8734 (mp) cc_final: 0.8468 (mp) REVERT: P 4 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8621 (tt) REVERT: U 4 LEU cc_start: 0.8761 (tt) cc_final: 0.8489 (tp) REVERT: Y 4 LEU cc_start: 0.8957 (tp) cc_final: 0.8715 (tp) REVERT: 1 4 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8436 (tt) REVERT: m 4 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8446 (tt) outliers start: 33 outliers final: 25 residues processed: 161 average time/residue: 0.0267 time to fit residues: 6.3035 Evaluate side-chains 182 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain R residue 2 LEU Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 9 residue 2 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.145462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.127422 restraints weight = 6077.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.131462 restraints weight = 2978.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133929 restraints weight = 1853.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135520 restraints weight = 1331.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.136521 restraints weight = 1051.328| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 3536 Z= 0.090 Angle : 1.016 8.705 4784 Z= 0.332 Chirality : 0.054 0.137 468 Planarity : 0.001 0.006 416 Dihedral : 24.091 59.869 1040 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 11.06 % Allowed : 56.25 % Favored : 32.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.20 (0.36), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.25 (0.27), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 3484) covalent geometry : angle 1.01564 / 0.33 ( 4784) Misc. bond : bond 0.00044 / 0.02 ( 52) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.073 Fit side-chains REVERT: B 4 LEU cc_start: 0.8647 (tp) cc_final: 0.8426 (tp) REVERT: I 4 LEU cc_start: 0.8622 (tp) cc_final: 0.8325 (tp) REVERT: P 4 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8475 (tt) REVERT: 1 4 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (tt) REVERT: 2 2 LEU cc_start: 0.8456 (pt) cc_final: 0.7295 (tp) REVERT: 8 3 LEU cc_start: 0.8491 (mp) cc_final: 0.8255 (mp) outliers start: 23 outliers final: 16 residues processed: 146 average time/residue: 0.0265 time to fit residues: 5.6472 Evaluate side-chains 158 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain R residue 2 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 9 residue 2 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131556 restraints weight = 6431.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.135827 restraints weight = 2919.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.138205 restraints weight = 1760.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.139816 restraints weight = 1267.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140916 restraints weight = 989.332| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.045 3536 Z= 0.712 Angle : 1.631 11.254 4784 Z= 0.577 Chirality : 0.069 0.175 468 Planarity : 0.003 0.007 416 Dihedral : 24.113 59.160 1040 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 12.02 % Allowed : 57.21 % Favored : 30.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.09 (0.43), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.16 (0.33), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01489 / 0.72 ( 3484) covalent geometry : angle 1.63071 / 0.58 ( 4784) Misc. bond : bond 0.00246 / 0.13 ( 52) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 LEU cc_start: 0.8830 (tp) cc_final: 0.8614 (tp) REVERT: G 5 LEU cc_start: 0.8827 (mm) cc_final: 0.8607 (mp) REVERT: I 4 LEU cc_start: 0.8817 (tp) cc_final: 0.8494 (tp) REVERT: J 3 LEU cc_start: 0.8749 (mp) cc_final: 0.8518 (mp) REVERT: U 4 LEU cc_start: 0.8768 (tt) cc_final: 0.8388 (tp) REVERT: 1 4 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8468 (tt) REVERT: 8 2 LEU cc_start: 0.9161 (pp) cc_final: 0.8937 (pt) outliers start: 25 outliers final: 21 residues processed: 158 average time/residue: 0.0290 time to fit residues: 6.6827 Evaluate side-chains 174 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain R residue 2 LEU Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain Z residue 2 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 3 LEU Chi-restraints excluded: chain 9 residue 2 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.145329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.127157 restraints weight = 6027.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131174 restraints weight = 2932.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.133540 restraints weight = 1818.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135115 restraints weight = 1319.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.135908 restraints weight = 1052.481| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3536 Z= 0.102 Angle : 1.032 8.991 4784 Z= 0.338 Chirality : 0.054 0.137 468 Planarity : 0.001 0.006 416 Dihedral : 24.132 59.841 1040 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.13 % Allowed : 59.62 % Favored : 31.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.02 (0.40), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.11 (0.31), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 3484) covalent geometry : angle 1.03230 / 0.34 ( 4784) Misc. bond : bond 0.00026 / 0.01 ( 52) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 208 Ramachandran restraints generated. 104 Oldfield, 0 Emsley, 104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.080 Fit side-chains REVERT: I 4 LEU cc_start: 0.8559 (tp) cc_final: 0.8238 (tp) REVERT: 1 4 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8283 (tt) REVERT: 8 2 LEU cc_start: 0.9104 (pp) cc_final: 0.8888 (pt) REVERT: i 2 LEU cc_start: 0.8659 (pt) cc_final: 0.7398 (tp) outliers start: 19 outliers final: 15 residues processed: 144 average time/residue: 0.0305 time to fit residues: 6.3533 Evaluate side-chains 155 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain R residue 2 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 9 residue 2 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.148439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131665 restraints weight = 6471.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135834 restraints weight = 2928.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138426 restraints weight = 1781.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.140108 restraints weight = 1263.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141172 restraints weight = 980.499| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.042 3536 Z= 0.709 Angle : 1.629 11.780 4784 Z= 0.576 Chirality : 0.069 0.181 468 Planarity : 0.003 0.007 416 Dihedral : 24.098 59.558 1040 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 9.62 % Allowed : 60.58 % Favored : 29.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.82 (0.51), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.95 (0.39), residues: 104 Details of bonding type rmsd/Z covalent geometry : bond 0.01481 / 0.71 ( 3484) covalent geometry : angle 1.62864 / 0.58 ( 4784) Misc. bond : bond 0.00249 / 0.13 ( 52) =============================================================================== Job complete usr+sys time: 415.49 seconds wall clock time: 7 minutes 50.79 seconds (470.79 seconds total)