Starting phenix.real_space_refine on Sat May 2 07:37:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9net_49335/05_2026/9net_49335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9net_49335/05_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_49335/05_2026/9net_49335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9net_49335/05_2026/9net_49335.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9net_49335/05_2026/9net_49335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9net_49335/05_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-2.1rc2-6044/lib/python3.9/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: 0.48, per 1000 atoms: 0.14 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: 0.42 Conformation dependent library (CDL) restraints added in 48.9 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: 0.31 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: 0.54 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: 2.770 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: 4.560 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 covalent geometry : bond 0.04285 ( 3484) covalent geometry : angle 7.42851 ( 4784) Misc. bond : bond 0.10717 ( 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 : 0.060 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: 0.0308 time to fit residues: 6.7834 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 : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.104433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.085347 restraints weight = 8364.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.087854 restraints weight = 5203.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.089423 restraints weight = 3861.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.090496 restraints weight = 3184.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091119 restraints weight = 2789.625| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.094 0.297 3536 Z= 4.483 Angle : 7.220 55.897 4784 Z= 2.585 Chirality : 0.250 0.741 468 Planarity : 0.015 0.053 416 Dihedral : 31.898 72.395 1040 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 68.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.81 % Favored : 70.19 % Rotamer: Outliers : 33.17 % Allowed : 34.62 % Favored : 32.21 % Cbeta Deviations : 1.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -10.18 (0.29), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.76 (0.22), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09420 ( 3484) covalent geometry : angle 7.21992 ( 4784) Misc. bond : bond 0.01021 ( 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 213 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 144 time to evaluate : 0.107 Fit side-chains REVERT: K 2 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8964 (pt) REVERT: R 2 LEU cc_start: 0.9373 (pt) cc_final: 0.9154 (pp) REVERT: 9 5 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8669 (tp) REVERT: f 2 LEU cc_start: 0.9272 (pt) cc_final: 0.9063 (pt) outliers start: 69 outliers final: 43 residues processed: 158 average time/residue: 0.0301 time to fit residues: 7.0286 Evaluate side-chains 186 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 4 LEU Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g 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 k residue 5 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.107025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087093 restraints weight = 8145.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.089467 restraints weight = 5244.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.090969 restraints weight = 4003.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091832 restraints weight = 3368.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.092684 restraints weight = 3015.250| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.8153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.293 3536 Z= 4.466 Angle : 7.210 55.793 4784 Z= 2.573 Chirality : 0.245 0.698 468 Planarity : 0.015 0.049 416 Dihedral : 31.563 78.818 1040 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 76.33 Ramachandran Plot: Outliers : 0.96 % Allowed : 43.27 % Favored : 55.77 % Rotamer: Outliers : 43.75 % Allowed : 33.65 % Favored : 22.60 % Cbeta Deviations : 2.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -10.66 (0.19), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.12 (0.15), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09375 ( 3484) covalent geometry : angle 7.21011 ( 4784) Misc. bond : bond 0.01017 ( 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 238 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 147 time to evaluate : 0.129 Fit side-chains REVERT: K 2 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8990 (pt) REVERT: N 5 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8991 (tt) REVERT: 1 4 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9072 (tt) REVERT: 9 5 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8634 (tp) REVERT: h 4 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9050 (tp) REVERT: m 4 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8858 (tp) outliers start: 91 outliers final: 61 residues processed: 175 average time/residue: 0.0311 time to fit residues: 8.0217 Evaluate side-chains 211 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 144 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H 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 K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 5 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o 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: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.111963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092212 restraints weight = 7796.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094284 restraints weight = 5066.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095599 restraints weight = 3906.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.096477 restraints weight = 3325.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096998 restraints weight = 2981.156| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.8259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.094 0.294 3536 Z= 4.471 Angle : 7.243 55.983 4784 Z= 2.581 Chirality : 0.246 0.702 468 Planarity : 0.015 0.049 416 Dihedral : 31.512 88.778 1040 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 75.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 37.50 % Favored : 62.50 % Rotamer: Outliers : 39.90 % Allowed : 37.50 % Favored : 22.60 % Cbeta Deviations : 2.69 % 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: -10.81 (0.16), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.24 (0.13), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09420 ( 3484) covalent geometry : angle 7.24272 ( 4784) Misc. bond : bond 0.01027 ( 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 235 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 152 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: K 2 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8908 (pt) REVERT: N 5 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8920 (tt) REVERT: Q 3 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8372 (pt) REVERT: T 4 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8921 (tt) REVERT: Y 5 LEU cc_start: 0.9521 (tp) cc_final: 0.9305 (tt) REVERT: 0 4 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8800 (tt) REVERT: 1 4 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8973 (tt) REVERT: 9 5 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8621 (tp) REVERT: h 4 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8893 (tp) REVERT: m 4 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8626 (tp) REVERT: o 4 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8995 (tt) outliers start: 83 outliers final: 65 residues processed: 176 average time/residue: 0.0305 time to fit residues: 7.9578 Evaluate side-chains 224 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 149 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 2 LEU Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 3 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 Chi-restraints excluded: chain o residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.109575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.091414 restraints weight = 8020.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093553 restraints weight = 5010.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094946 restraints weight = 3754.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095827 restraints weight = 3125.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096426 restraints weight = 2779.004| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.8309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.295 3536 Z= 4.473 Angle : 7.262 55.426 4784 Z= 2.582 Chirality : 0.245 0.730 468 Planarity : 0.015 0.049 416 Dihedral : 31.413 88.784 1040 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 74.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 47.12 % Favored : 52.88 % Rotamer: Outliers : 42.31 % Allowed : 35.10 % Favored : 22.60 % Cbeta Deviations : 3.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -10.90 (0.14), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.31 (0.11), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09396 ( 3484) covalent geometry : angle 7.26227 ( 4784) Misc. bond : bond 0.01031 ( 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 239 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 151 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: K 2 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8903 (pt) REVERT: N 5 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8945 (tt) REVERT: O 4 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8791 (tt) REVERT: Q 3 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8438 (pt) REVERT: T 4 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8932 (tt) REVERT: W 4 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8722 (tt) REVERT: Y 5 LEU cc_start: 0.9523 (tp) cc_final: 0.9295 (tt) REVERT: 0 4 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8807 (tt) REVERT: 1 4 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9017 (tt) REVERT: 8 4 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8696 (tt) REVERT: 9 5 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8635 (tp) REVERT: h 4 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8881 (tp) REVERT: m 4 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8802 (tp) REVERT: o 4 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9024 (tt) outliers start: 88 outliers final: 68 residues processed: 177 average time/residue: 0.0297 time to fit residues: 7.6966 Evaluate side-chains 231 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 150 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H 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 K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 2 LEU Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 3 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.110378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.091905 restraints weight = 8020.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093971 restraints weight = 5094.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.095298 restraints weight = 3864.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096297 restraints weight = 3230.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096902 restraints weight = 2826.396| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.8330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.295 3536 Z= 4.466 Angle : 7.260 55.994 4784 Z= 2.583 Chirality : 0.243 0.697 468 Planarity : 0.015 0.049 416 Dihedral : 31.339 86.825 1040 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 77.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.38 % Favored : 59.62 % Rotamer: Outliers : 42.79 % Allowed : 36.06 % Favored : 21.15 % Cbeta Deviations : 3.46 % 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: -10.91 (0.13), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.31 (0.10), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09371 ( 3484) covalent geometry : angle 7.25960 ( 4784) Misc. bond : bond 0.01006 ( 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 240 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 151 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: K 2 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8913 (pt) REVERT: N 5 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8948 (tt) REVERT: O 4 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8775 (tt) REVERT: Q 3 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8403 (pt) REVERT: T 4 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8951 (tt) REVERT: W 4 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8733 (tt) REVERT: Y 5 LEU cc_start: 0.9537 (tp) cc_final: 0.9310 (tt) REVERT: 0 4 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8822 (tt) REVERT: 1 4 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9042 (tt) REVERT: 9 5 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8659 (tp) REVERT: h 4 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8893 (tp) REVERT: i 3 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8674 (pt) REVERT: m 4 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8820 (tp) REVERT: o 4 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9040 (tt) outliers start: 89 outliers final: 70 residues processed: 178 average time/residue: 0.0311 time to fit residues: 8.0886 Evaluate side-chains 233 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 150 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H 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 K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 2 LEU Chi-restraints excluded: chain 6 residue 4 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 3 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 3 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 2 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.107638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088509 restraints weight = 8263.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090590 restraints weight = 5437.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091868 restraints weight = 4232.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092677 restraints weight = 3627.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093337 restraints weight = 3255.207| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.8360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.295 3536 Z= 4.463 Angle : 7.258 55.897 4784 Z= 2.583 Chirality : 0.242 0.688 468 Planarity : 0.015 0.050 416 Dihedral : 31.310 88.279 1040 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 76.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 46.15 % Favored : 53.85 % Rotamer: Outliers : 43.75 % Allowed : 39.90 % Favored : 16.35 % Cbeta Deviations : 3.46 % 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: -10.97 (0.12), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.36 (0.09), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09357 ( 3484) covalent geometry : angle 7.25781 ( 4784) Misc. bond : bond 0.01005 ( 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 241 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 150 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: E 2 LEU cc_start: 0.9242 (pp) cc_final: 0.8949 (pt) REVERT: K 2 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8896 (pt) REVERT: N 5 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8912 (tt) REVERT: O 4 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8706 (tt) REVERT: Q 3 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8412 (pt) REVERT: T 4 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8900 (tt) REVERT: W 4 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8658 (tt) REVERT: Y 5 LEU cc_start: 0.9501 (tp) cc_final: 0.9288 (tt) REVERT: 0 4 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8752 (tt) REVERT: 1 4 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9010 (tt) REVERT: 9 5 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8601 (tp) REVERT: h 4 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8857 (tp) REVERT: i 3 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8675 (pt) REVERT: m 4 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8741 (tp) REVERT: o 4 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9000 (tt) outliers start: 91 outliers final: 70 residues processed: 177 average time/residue: 0.0304 time to fit residues: 7.9372 Evaluate side-chains 232 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 149 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H 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 K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 2 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 3 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 3 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.109482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091028 restraints weight = 8077.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093179 restraints weight = 5057.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094553 restraints weight = 3803.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095409 restraints weight = 3173.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096111 restraints weight = 2809.439| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.8383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.294 3536 Z= 4.462 Angle : 7.264 55.793 4784 Z= 2.585 Chirality : 0.243 0.683 468 Planarity : 0.015 0.050 416 Dihedral : 31.280 89.158 1040 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 78.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 42.31 % Favored : 57.69 % Rotamer: Outliers : 44.23 % Allowed : 38.94 % Favored : 16.83 % Cbeta Deviations : 3.46 % 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: -10.92 (0.12), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.32 (0.09), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09363 ( 3484) covalent geometry : angle 7.26379 ( 4784) Misc. bond : bond 0.01010 ( 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 244 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 152 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: K 2 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8901 (pt) REVERT: N 5 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8930 (tt) REVERT: O 4 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8756 (tt) REVERT: Q 3 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8410 (pt) REVERT: T 4 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8941 (tt) REVERT: W 4 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8729 (tt) REVERT: Y 5 LEU cc_start: 0.9527 (tp) cc_final: 0.9305 (tt) REVERT: 0 4 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8788 (tt) REVERT: 1 4 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9036 (tt) REVERT: 8 4 LEU cc_start: 0.9063 (tp) cc_final: 0.8655 (tt) REVERT: 9 5 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8601 (tp) REVERT: h 4 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8868 (tp) REVERT: i 3 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8676 (pt) REVERT: m 4 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8759 (tp) REVERT: o 4 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9024 (tt) outliers start: 92 outliers final: 74 residues processed: 179 average time/residue: 0.0293 time to fit residues: 7.7043 Evaluate side-chains 238 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 151 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H 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 K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 2 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 3 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 3 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.109874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091317 restraints weight = 8059.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093416 restraints weight = 5113.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094815 restraints weight = 3889.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.095726 restraints weight = 3262.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096401 restraints weight = 2892.190| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.8400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.295 3536 Z= 4.465 Angle : 7.272 55.890 4784 Z= 2.590 Chirality : 0.244 0.672 468 Planarity : 0.015 0.052 416 Dihedral : 31.259 87.042 1040 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 78.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.19 % Favored : 54.81 % Rotamer: Outliers : 44.23 % Allowed : 41.83 % Favored : 13.94 % Cbeta Deviations : 3.46 % 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: -10.96 (0.12), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.35 (0.09), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09374 ( 3484) covalent geometry : angle 7.27199 ( 4784) Misc. bond : bond 0.00994 ( 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 243 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 151 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: K 2 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8945 (pt) REVERT: N 5 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8955 (tt) REVERT: O 4 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8794 (tt) REVERT: Q 3 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8399 (pt) REVERT: T 4 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8969 (tt) REVERT: W 4 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8807 (tt) REVERT: Y 5 LEU cc_start: 0.9520 (tp) cc_final: 0.9315 (tt) REVERT: 0 4 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8801 (tt) REVERT: 1 4 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9044 (tt) REVERT: 9 5 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8594 (tp) REVERT: h 4 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8880 (tp) REVERT: i 3 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8674 (pt) REVERT: m 4 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8798 (tp) REVERT: o 4 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9072 (tt) outliers start: 92 outliers final: 73 residues processed: 178 average time/residue: 0.0310 time to fit residues: 8.0961 Evaluate side-chains 237 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 151 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H 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 K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 2 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 3 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 3 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.109441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.090798 restraints weight = 8106.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.092965 restraints weight = 5141.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094431 restraints weight = 3895.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.095292 restraints weight = 3244.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.096012 restraints weight = 2873.439| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.8398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.295 3536 Z= 4.462 Angle : 7.280 55.791 4784 Z= 2.593 Chirality : 0.244 0.672 468 Planarity : 0.015 0.052 416 Dihedral : 31.229 86.869 1040 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 78.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 44.23 % Favored : 55.77 % Rotamer: Outliers : 42.31 % Allowed : 45.19 % Favored : 12.50 % Cbeta Deviations : 3.85 % 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: -10.93 (0.12), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.33 (0.09), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09375 ( 3484) covalent geometry : angle 7.28016 ( 4784) Misc. bond : bond 0.01004 ( 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 238 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 150 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: K 2 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8923 (pt) REVERT: N 5 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8953 (tt) REVERT: O 4 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8791 (tt) REVERT: Q 3 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8431 (pt) REVERT: T 4 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8970 (tt) REVERT: W 4 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8782 (tt) REVERT: 0 4 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8800 (tt) REVERT: 1 4 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9029 (tt) REVERT: 9 5 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8621 (tp) REVERT: h 4 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8883 (tp) REVERT: i 3 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8674 (pt) REVERT: m 4 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8782 (tp) REVERT: n 4 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9159 (tt) REVERT: o 4 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9081 (tt) outliers start: 88 outliers final: 71 residues processed: 174 average time/residue: 0.0304 time to fit residues: 7.7547 Evaluate side-chains 235 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 150 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H 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 K residue 2 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain 0 residue 4 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 2 residue 3 LEU Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 4 residue 5 LEU Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 6 residue 2 LEU Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 7 residue 5 LEU Chi-restraints excluded: chain 8 residue 5 LEU Chi-restraints excluded: chain 9 residue 5 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 5 LEU Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 3 LEU Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain e residue 2 LEU Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 2 LEU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 5 LEU Chi-restraints excluded: chain i residue 2 LEU Chi-restraints excluded: chain i residue 3 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 k residue 5 LEU Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 5 LEU Chi-restraints excluded: chain m residue 3 LEU Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain o residue 4 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090946 restraints weight = 8263.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.093124 restraints weight = 5252.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094556 restraints weight = 3943.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095560 restraints weight = 3277.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096146 restraints weight = 2885.228| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.8424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.093 0.295 3536 Z= 4.466 Angle : 7.286 55.850 4784 Z= 2.595 Chirality : 0.245 0.666 468 Planarity : 0.015 0.051 416 Dihedral : 31.232 87.671 1040 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 79.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 47.12 % Favored : 52.88 % Rotamer: Outliers : 42.79 % Allowed : 43.75 % Favored : 13.46 % Cbeta Deviations : 3.46 % 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: -10.95 (0.12), residues: 104 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.34 (0.09), residues: 104 Details of bonding type rmsd covalent geometry : bond 0.09377 ( 3484) covalent geometry : angle 7.28621 ( 4784) Misc. bond : bond 0.01022 ( 52) =============================================================================== Job complete usr+sys time: 438.23 seconds wall clock time: 8 minutes 17.65 seconds (497.65 seconds total)