Starting phenix.real_space_refine on Tue Feb 3 14:42:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rbw_53910/02_2026/9rbw_53910.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rbw_53910/02_2026/9rbw_53910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rbw_53910/02_2026/9rbw_53910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rbw_53910/02_2026/9rbw_53910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rbw_53910/02_2026/9rbw_53910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rbw_53910/02_2026/9rbw_53910.map" } resolution = 3.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 2330 2.51 5 N 840 2.21 5 O 715 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3945 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 189 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "E" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "G" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 189 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "H" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "I" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 189 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "L" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "N" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "O" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 189 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "P" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "Q" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "R" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Chain: "S" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 189 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "T" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 200 Classifications: {'peptide': 26} Modifications used: {'COO': 1} Link IDs: {'TRANS': 25} Time building chain proxies: 1.22, per 1000 atoms: 0.31 Number of scatterers: 3945 At special positions: 0 Unit cell: (83.0292, 108.19, 45.2887, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 715 8.00 N 840 7.00 C 2330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=1.93 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS D 23 " distance=2.04 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS A 7 " distance=2.15 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS A 23 " distance=1.95 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS F 7 " distance=1.96 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS F 23 " distance=2.08 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS H 7 " distance=2.10 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS H 23 " distance=2.05 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS J 7 " distance=2.16 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS J 23 " distance=1.77 Simple disulfide: pdb=" SG CYS K 7 " - pdb=" SG CYS L 7 " distance=2.14 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS L 23 " distance=2.15 Simple disulfide: pdb=" SG CYS M 7 " - pdb=" SG CYS N 7 " distance=2.18 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS N 23 " distance=2.01 Simple disulfide: pdb=" SG CYS O 7 " - pdb=" SG CYS P 7 " distance=1.92 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS P 23 " distance=1.92 Simple disulfide: pdb=" SG CYS Q 7 " - pdb=" SG CYS R 7 " distance=1.80 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS R 23 " distance=2.35 Simple disulfide: pdb=" SG CYS S 7 " - pdb=" SG CYS T 7 " distance=2.04 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS T 23 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 183.3 milliseconds 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 830 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 19 through 21 removed outlier: 6.716A pdb=" N GLY I 20 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY C 20 " --> pdb=" O LEU I 21 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY Q 20 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER M 19 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 19 through 21 removed outlier: 6.963A pdb=" N LEU K 21 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY B 20 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY S 20 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY O 20 " --> pdb=" O LEU S 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 13 5 hydrogen bonds defined for protein. 15 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1180 1.33 - 1.45: 779 1.45 - 1.57: 1946 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 3985 Sorted by residual: bond pdb=" CA SER R 19 " pdb=" CB SER R 19 " ideal model delta sigma weight residual 1.530 1.494 0.036 1.55e-02 4.16e+03 5.54e+00 bond pdb=" CA SER N 19 " pdb=" CB SER N 19 " ideal model delta sigma weight residual 1.530 1.494 0.036 1.55e-02 4.16e+03 5.39e+00 bond pdb=" N ASN D 24 " pdb=" CA ASN D 24 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.23e-02 6.61e+03 5.10e+00 bond pdb=" C SER R 19 " pdb=" O SER R 19 " ideal model delta sigma weight residual 1.235 1.210 0.025 1.18e-02 7.18e+03 4.37e+00 bond pdb=" C SER R 19 " pdb=" N GLY R 20 " ideal model delta sigma weight residual 1.329 1.310 0.019 9.70e-03 1.06e+04 3.71e+00 ... (remaining 3980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 4574 0.79 - 1.57: 552 1.57 - 2.36: 42 2.36 - 3.15: 46 3.15 - 3.93: 16 Bond angle restraints: 5230 Sorted by residual: angle pdb=" C GLY L 20 " pdb=" N LEU L 21 " pdb=" CA LEU L 21 " ideal model delta sigma weight residual 123.03 119.73 3.30 1.34e+00 5.57e-01 6.06e+00 angle pdb=" CA LEU D 21 " pdb=" C LEU D 21 " pdb=" O LEU D 21 " ideal model delta sigma weight residual 121.94 118.01 3.93 1.68e+00 3.54e-01 5.48e+00 angle pdb=" CA LEU R 21 " pdb=" C LEU R 21 " pdb=" O LEU R 21 " ideal model delta sigma weight residual 121.94 118.17 3.77 1.68e+00 3.54e-01 5.04e+00 angle pdb=" C SER E 6 " pdb=" N CYS E 7 " pdb=" CA CYS E 7 " ideal model delta sigma weight residual 121.18 117.55 3.63 1.64e+00 3.72e-01 4.91e+00 angle pdb=" C SER K 6 " pdb=" N CYS K 7 " pdb=" CA CYS K 7 " ideal model delta sigma weight residual 121.18 117.56 3.62 1.64e+00 3.72e-01 4.87e+00 ... (remaining 5225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.71: 2074 10.71 - 21.42: 212 21.42 - 32.13: 96 32.13 - 42.84: 23 42.84 - 53.54: 15 Dihedral angle restraints: 2420 sinusoidal: 1075 harmonic: 1345 Sorted by residual: dihedral pdb=" N ASN D 24 " pdb=" CA ASN D 24 " pdb=" CB ASN D 24 " pdb=" CG ASN D 24 " ideal model delta sinusoidal sigma weight residual -60.00 -6.46 -53.54 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CB CYS O 7 " pdb=" SG CYS O 7 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 68.30 24.70 1 1.00e+01 1.00e-02 8.78e+00 dihedral pdb=" CA CYS K 7 " pdb=" CB CYS K 7 " pdb=" SG CYS K 7 " pdb=" SG CYS L 7 " ideal model delta sinusoidal sigma weight residual 183.00 132.39 50.61 1 2.00e+01 2.50e-03 8.77e+00 ... (remaining 2417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 280 0.027 - 0.054: 111 0.054 - 0.081: 34 0.081 - 0.108: 10 0.108 - 0.135: 20 Chirality restraints: 455 Sorted by residual: chirality pdb=" CA CYS M 7 " pdb=" N CYS M 7 " pdb=" C CYS M 7 " pdb=" CB CYS M 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA CYS S 7 " pdb=" N CYS S 7 " pdb=" C CYS S 7 " pdb=" CB CYS S 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA CYS K 7 " pdb=" N CYS K 7 " pdb=" C CYS K 7 " pdb=" CB CYS K 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 452 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 21 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C LEU L 21 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU L 21 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY L 22 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 21 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU A 21 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 21 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY A 22 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 21 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LEU H 21 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU H 21 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY H 22 " 0.019 2.00e-02 2.50e+03 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 939 2.78 - 3.31: 3396 3.31 - 3.84: 6189 3.84 - 4.37: 7640 4.37 - 4.90: 14231 Nonbonded interactions: 32395 Sorted by model distance: nonbonded pdb=" OG SER A 19 " pdb=" O SER L 19 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR C 28 " pdb=" O GLY B 22 " model vdw 2.267 3.040 nonbonded pdb=" OG SER B 19 " pdb=" O LEU L 21 " model vdw 2.278 3.040 nonbonded pdb=" OG SER O 19 " pdb=" O LEU T 21 " model vdw 2.290 3.040 nonbonded pdb=" OG SER C 19 " pdb=" O LEU J 21 " model vdw 2.296 3.040 ... (remaining 32390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 28) selection = chain 'B' selection = (chain 'C' and resid 4 through 28) selection = (chain 'D' and resid 4 through 28) selection = (chain 'E' and resid 4 through 28) selection = (chain 'F' and resid 4 through 28) selection = chain 'G' selection = (chain 'H' and resid 4 through 28) selection = (chain 'I' and resid 4 through 28) selection = (chain 'J' and resid 4 through 28) selection = chain 'K' selection = (chain 'L' and resid 4 through 28) selection = (chain 'M' and resid 4 through 28) selection = (chain 'N' and resid 4 through 28) selection = chain 'O' selection = (chain 'P' and resid 4 through 28) selection = (chain 'Q' and resid 4 through 28) selection = (chain 'R' and resid 4 through 28) selection = chain 'S' selection = (chain 'T' and resid 4 through 28) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.230 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 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 : 0.010 0.318 4005 Z= 0.496 Angle : 0.985 21.698 5270 Z= 0.508 Chirality : 0.040 0.135 455 Planarity : 0.004 0.044 730 Dihedral : 10.672 53.545 1530 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 5.06 % Allowed : 6.33 % Favored : 88.61 % 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: -5.16 (0.24), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.18), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 3 TYR 0.002 0.000 TYR L 28 PHE 0.011 0.002 PHE J 8 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3985) covalent geometry : angle 0.56545 ( 5230) SS BOND : bond 0.13290 ( 20) SS BOND : angle 9.27574 ( 40) hydrogen bonds : bond 0.13213 ( 5) hydrogen bonds : angle 8.96740 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 11 ARG cc_start: 0.6624 (mmm-85) cc_final: 0.6213 (tpm170) REVERT: G 14 ARG cc_start: 0.6972 (mtt90) cc_final: 0.6729 (ttp-170) REVERT: H 4 ARG cc_start: 0.7243 (mtp85) cc_final: 0.6393 (tmt-80) REVERT: J 18 GLN cc_start: 0.7700 (mt0) cc_final: 0.7434 (mt0) REVERT: L 18 GLN cc_start: 0.6994 (mt0) cc_final: 0.6741 (mt0) REVERT: M 3 ARG cc_start: 0.6667 (mtt180) cc_final: 0.5365 (ptt90) REVERT: P 4 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7081 (mtm-85) REVERT: T 23 CYS cc_start: 0.5249 (OUTLIER) cc_final: 0.4899 (m) REVERT: T 27 ARG cc_start: 0.6765 (ttt90) cc_final: 0.6504 (mtt-85) outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 0.1229 time to fit residues: 17.9396 Evaluate side-chains 98 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 24 ASN Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain T residue 23 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN B 18 GLN E 18 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN I 18 GLN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 GLN L 24 ASN M 18 GLN ** N 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 GLN Q 24 ASN S 18 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.177798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.162949 restraints weight = 4888.957| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 2.13 r_work: 0.4549 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4450 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4005 Z= 0.190 Angle : 0.714 7.818 5270 Z= 0.385 Chirality : 0.045 0.159 455 Planarity : 0.004 0.025 730 Dihedral : 7.941 56.762 647 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 3.54 % Allowed : 15.95 % Favored : 80.51 % 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: -5.31 (0.24), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.18), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 27 TYR 0.012 0.002 TYR Q 28 PHE 0.025 0.002 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3985) covalent geometry : angle 0.70013 ( 5230) SS BOND : bond 0.00490 ( 20) SS BOND : angle 1.75064 ( 40) hydrogen bonds : bond 0.01168 ( 5) hydrogen bonds : angle 4.62180 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: D 18 GLN cc_start: 0.7496 (mt0) cc_final: 0.7012 (mt0) REVERT: B 14 ARG cc_start: 0.7853 (mtt90) cc_final: 0.6850 (tpt90) REVERT: E 12 MET cc_start: 0.7575 (ttm) cc_final: 0.7354 (ttm) REVERT: F 13 ASP cc_start: 0.7824 (p0) cc_final: 0.7359 (p0) REVERT: G 11 ARG cc_start: 0.7111 (mmm-85) cc_final: 0.5775 (tpm170) REVERT: G 14 ARG cc_start: 0.7775 (mtt90) cc_final: 0.6353 (ttp-170) REVERT: H 4 ARG cc_start: 0.7310 (mtp85) cc_final: 0.6343 (tmt-80) REVERT: H 15 ILE cc_start: 0.8550 (mm) cc_final: 0.8213 (mm) REVERT: H 24 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7822 (m110) REVERT: I 5 SER cc_start: 0.7380 (m) cc_final: 0.6788 (p) REVERT: K 12 MET cc_start: 0.6949 (mtp) cc_final: 0.6670 (mpp) REVERT: K 27 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.7095 (ttm110) REVERT: M 3 ARG cc_start: 0.6795 (mtt180) cc_final: 0.5017 (ptt90) REVERT: M 27 ARG cc_start: 0.7385 (ttm110) cc_final: 0.6440 (tpm170) REVERT: N 15 ILE cc_start: 0.8910 (mm) cc_final: 0.8657 (mt) REVERT: R 27 ARG cc_start: 0.7784 (ttt90) cc_final: 0.7435 (tmt170) REVERT: T 15 ILE cc_start: 0.8431 (mm) cc_final: 0.8000 (mm) REVERT: T 27 ARG cc_start: 0.7538 (ttt90) cc_final: 0.7134 (mtt-85) outliers start: 14 outliers final: 8 residues processed: 111 average time/residue: 0.1105 time to fit residues: 13.8670 Evaluate side-chains 99 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain P residue 24 ASN Chi-restraints excluded: chain Q residue 24 ASN Chi-restraints excluded: chain R residue 24 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN N 24 ASN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.165065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.151314 restraints weight = 4652.435| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 1.98 r_work: 0.4400 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4292 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 4005 Z= 0.418 Angle : 1.015 6.413 5270 Z= 0.551 Chirality : 0.056 0.203 455 Planarity : 0.007 0.049 730 Dihedral : 9.963 63.067 640 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 8.61 % Allowed : 19.24 % Favored : 72.15 % 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: -5.52 (0.24), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.18), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 3 TYR 0.018 0.003 TYR E 28 PHE 0.026 0.003 PHE J 26 Details of bonding type rmsd covalent geometry : bond 0.00932 ( 3985) covalent geometry : angle 0.99578 ( 5230) SS BOND : bond 0.00806 ( 20) SS BOND : angle 2.48406 ( 40) hydrogen bonds : bond 0.01409 ( 5) hydrogen bonds : angle 6.43344 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7637 (m) cc_final: 0.6747 (t) REVERT: D 12 MET cc_start: 0.8560 (mtt) cc_final: 0.8354 (mtt) REVERT: D 18 GLN cc_start: 0.7669 (mt0) cc_final: 0.6937 (mt0) REVERT: A 25 SER cc_start: 0.8620 (t) cc_final: 0.8418 (t) REVERT: E 3 ARG cc_start: 0.4964 (mtt180) cc_final: 0.4505 (mmp-170) REVERT: E 12 MET cc_start: 0.7776 (ttm) cc_final: 0.7494 (ttm) REVERT: F 28 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.7086 (m-10) REVERT: G 11 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.5979 (tpm170) REVERT: H 4 ARG cc_start: 0.7511 (mtp85) cc_final: 0.6412 (tmt-80) REVERT: H 14 ARG cc_start: 0.6593 (tpm170) cc_final: 0.4711 (mtt-85) REVERT: H 24 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7971 (m110) REVERT: I 3 ARG cc_start: 0.6448 (ttm-80) cc_final: 0.5832 (mtp180) REVERT: I 5 SER cc_start: 0.7660 (m) cc_final: 0.6809 (p) REVERT: K 12 MET cc_start: 0.7273 (mtp) cc_final: 0.6863 (mpp) REVERT: L 19 SER cc_start: 0.9170 (m) cc_final: 0.8707 (p) REVERT: M 3 ARG cc_start: 0.6676 (mtt180) cc_final: 0.4880 (ptt90) REVERT: M 11 ARG cc_start: 0.7211 (mmm-85) cc_final: 0.6239 (ttp-170) REVERT: M 27 ARG cc_start: 0.7473 (ttm110) cc_final: 0.6016 (mmp80) REVERT: N 13 ASP cc_start: 0.7898 (p0) cc_final: 0.7656 (p0) REVERT: N 15 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8756 (mt) REVERT: O 18 GLN cc_start: 0.6732 (mt0) cc_final: 0.5910 (mp10) REVERT: P 15 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8563 (mm) REVERT: Q 27 ARG cc_start: 0.7183 (ttm-80) cc_final: 0.6669 (ttm170) REVERT: R 27 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7510 (tmt170) outliers start: 34 outliers final: 25 residues processed: 122 average time/residue: 0.0959 time to fit residues: 13.2927 Evaluate side-chains 121 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 28 TYR Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 24 ASN Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain Q residue 24 ASN Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain S residue 7 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 ASN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN Q 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.179811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.166004 restraints weight = 4354.808| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 2.04 r_work: 0.4542 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4441 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4005 Z= 0.135 Angle : 0.673 6.333 5270 Z= 0.354 Chirality : 0.042 0.135 455 Planarity : 0.003 0.026 730 Dihedral : 8.746 62.601 640 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 5.32 % Allowed : 21.77 % Favored : 72.91 % 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: -5.53 (0.23), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.18), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 11 TYR 0.015 0.001 TYR E 28 PHE 0.016 0.002 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3985) covalent geometry : angle 0.66375 ( 5230) SS BOND : bond 0.00319 ( 20) SS BOND : angle 1.44270 ( 40) hydrogen bonds : bond 0.00626 ( 5) hydrogen bonds : angle 5.18702 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7605 (m) cc_final: 0.6690 (t) REVERT: C 14 ARG cc_start: 0.8036 (mtt90) cc_final: 0.6557 (tpt90) REVERT: D 18 GLN cc_start: 0.7353 (mt0) cc_final: 0.6893 (mt0) REVERT: B 14 ARG cc_start: 0.7960 (mtt90) cc_final: 0.6568 (tpt90) REVERT: E 3 ARG cc_start: 0.4874 (mtt180) cc_final: 0.4442 (mmp-170) REVERT: E 11 ARG cc_start: 0.4314 (tpp-160) cc_final: 0.3592 (tpp-160) REVERT: E 12 MET cc_start: 0.7549 (ttm) cc_final: 0.7238 (ttm) REVERT: F 13 ASP cc_start: 0.7893 (p0) cc_final: 0.7320 (p0) REVERT: G 11 ARG cc_start: 0.7133 (mmm-85) cc_final: 0.5779 (tpm170) REVERT: H 4 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6336 (tmt-80) REVERT: H 24 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7698 (m110) REVERT: I 3 ARG cc_start: 0.6348 (ttm-80) cc_final: 0.5792 (mtp180) REVERT: I 5 SER cc_start: 0.7444 (m) cc_final: 0.6446 (p) REVERT: K 12 MET cc_start: 0.6917 (mtp) cc_final: 0.6695 (mpp) REVERT: K 28 TYR cc_start: 0.8183 (m-80) cc_final: 0.7933 (m-80) REVERT: L 19 SER cc_start: 0.9028 (m) cc_final: 0.8671 (p) REVERT: M 3 ARG cc_start: 0.6576 (mtt180) cc_final: 0.4895 (ptt90) REVERT: M 11 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6513 (ttp-110) REVERT: M 27 ARG cc_start: 0.7327 (ttm110) cc_final: 0.6133 (mmp80) REVERT: N 13 ASP cc_start: 0.7790 (p0) cc_final: 0.7573 (p0) REVERT: R 24 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8314 (p0) REVERT: R 27 ARG cc_start: 0.7808 (ttt90) cc_final: 0.7390 (tmt170) REVERT: T 27 ARG cc_start: 0.7560 (ttt90) cc_final: 0.7003 (mtt-85) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.1017 time to fit residues: 14.3257 Evaluate side-chains 111 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain Q residue 24 ASN Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain S residue 7 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 ASN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN N 24 ASN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.170176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.156383 restraints weight = 4590.412| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 1.99 r_work: 0.4445 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4341 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4005 Z= 0.277 Angle : 0.801 5.970 5270 Z= 0.432 Chirality : 0.048 0.158 455 Planarity : 0.005 0.036 730 Dihedral : 8.862 70.931 636 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.21 % Favored : 79.79 % Rotamer: Outliers : 7.85 % Allowed : 21.52 % Favored : 70.63 % 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: -5.62 (0.23), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.18), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 11 TYR 0.015 0.002 TYR Q 28 PHE 0.022 0.003 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 3985) covalent geometry : angle 0.78521 ( 5230) SS BOND : bond 0.00534 ( 20) SS BOND : angle 1.98833 ( 40) hydrogen bonds : bond 0.00924 ( 5) hydrogen bonds : angle 5.67172 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7766 (m) cc_final: 0.6839 (t) REVERT: D 18 GLN cc_start: 0.7496 (mt0) cc_final: 0.6915 (mt0) REVERT: B 14 ARG cc_start: 0.8074 (mtt90) cc_final: 0.6577 (tpt90) REVERT: A 25 SER cc_start: 0.8589 (t) cc_final: 0.8369 (t) REVERT: E 3 ARG cc_start: 0.4877 (mtt180) cc_final: 0.4451 (mmp-170) REVERT: E 12 MET cc_start: 0.7731 (ttm) cc_final: 0.7381 (ttm) REVERT: F 13 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7296 (p0) REVERT: G 11 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.5954 (tpm170) REVERT: H 4 ARG cc_start: 0.7482 (mtp85) cc_final: 0.6409 (tmt-80) REVERT: I 3 ARG cc_start: 0.6487 (ttm-80) cc_final: 0.5842 (mtp180) REVERT: I 5 SER cc_start: 0.7588 (m) cc_final: 0.6613 (p) REVERT: K 12 MET cc_start: 0.7241 (mtp) cc_final: 0.6891 (mpp) REVERT: L 19 SER cc_start: 0.9136 (m) cc_final: 0.8725 (p) REVERT: M 3 ARG cc_start: 0.6629 (mtt180) cc_final: 0.4834 (ptt90) REVERT: M 11 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6435 (ttp-110) REVERT: M 27 ARG cc_start: 0.7401 (ttm110) cc_final: 0.6128 (mmp80) REVERT: N 13 ASP cc_start: 0.7857 (p0) cc_final: 0.7547 (p0) REVERT: N 15 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8788 (mt) REVERT: O 14 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7935 (mtm-85) REVERT: O 18 GLN cc_start: 0.6648 (mt0) cc_final: 0.5805 (mp10) REVERT: P 15 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8508 (mm) REVERT: R 27 ARG cc_start: 0.7917 (ttt90) cc_final: 0.7449 (tmt170) REVERT: T 27 ARG cc_start: 0.7609 (ttt90) cc_final: 0.6989 (mtt-85) outliers start: 31 outliers final: 21 residues processed: 117 average time/residue: 0.1048 time to fit residues: 14.0441 Evaluate side-chains 114 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain S residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 ASN ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.176574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.162809 restraints weight = 4497.668| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 2.05 r_work: 0.4506 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4402 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4005 Z= 0.166 Angle : 0.681 5.712 5270 Z= 0.364 Chirality : 0.043 0.140 455 Planarity : 0.004 0.037 730 Dihedral : 8.191 72.635 632 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 6.58 % Allowed : 22.53 % Favored : 70.89 % 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: -5.64 (0.23), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.17), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 11 TYR 0.016 0.002 TYR E 28 PHE 0.021 0.002 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3985) covalent geometry : angle 0.66987 ( 5230) SS BOND : bond 0.00325 ( 20) SS BOND : angle 1.58414 ( 40) hydrogen bonds : bond 0.00988 ( 5) hydrogen bonds : angle 5.74901 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7716 (m) cc_final: 0.6833 (t) REVERT: D 18 GLN cc_start: 0.7369 (mt0) cc_final: 0.6953 (mt0) REVERT: B 14 ARG cc_start: 0.8089 (mtt90) cc_final: 0.6589 (tpt90) REVERT: E 3 ARG cc_start: 0.4931 (mtt180) cc_final: 0.4472 (mmp-170) REVERT: E 11 ARG cc_start: 0.4333 (tpp-160) cc_final: 0.3578 (tpp-160) REVERT: E 12 MET cc_start: 0.7658 (ttm) cc_final: 0.7337 (ttm) REVERT: F 13 ASP cc_start: 0.7744 (p0) cc_final: 0.7176 (p0) REVERT: G 11 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.5835 (tpm170) REVERT: H 4 ARG cc_start: 0.7407 (mtp85) cc_final: 0.6452 (tmt-80) REVERT: H 19 SER cc_start: 0.8626 (m) cc_final: 0.8258 (p) REVERT: I 3 ARG cc_start: 0.6413 (ttm-80) cc_final: 0.5779 (mtp180) REVERT: I 5 SER cc_start: 0.7343 (m) cc_final: 0.6376 (p) REVERT: K 12 MET cc_start: 0.7154 (mtp) cc_final: 0.6832 (mpp) REVERT: L 19 SER cc_start: 0.9047 (m) cc_final: 0.8819 (p) REVERT: M 3 ARG cc_start: 0.6541 (mtt180) cc_final: 0.4742 (ppt170) REVERT: M 11 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6432 (ttp-110) REVERT: M 27 ARG cc_start: 0.7373 (ttm110) cc_final: 0.6139 (mmp80) REVERT: N 15 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8768 (mt) REVERT: P 15 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8435 (mm) REVERT: R 27 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7374 (tmt170) REVERT: T 27 ARG cc_start: 0.7441 (ttt90) cc_final: 0.6893 (mtt-85) outliers start: 26 outliers final: 21 residues processed: 117 average time/residue: 0.1078 time to fit residues: 14.3093 Evaluate side-chains 117 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain S residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.179031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.165144 restraints weight = 4480.467| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 2.07 r_work: 0.4539 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4435 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4005 Z= 0.146 Angle : 0.640 5.612 5270 Z= 0.342 Chirality : 0.041 0.135 455 Planarity : 0.003 0.042 730 Dihedral : 7.845 73.497 632 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 7.09 % Allowed : 22.03 % Favored : 70.89 % 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: -5.63 (0.23), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.17), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 11 TYR 0.012 0.001 TYR E 28 PHE 0.019 0.002 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3985) covalent geometry : angle 0.63003 ( 5230) SS BOND : bond 0.00283 ( 20) SS BOND : angle 1.43084 ( 40) hydrogen bonds : bond 0.01065 ( 5) hydrogen bonds : angle 5.44053 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7687 (m) cc_final: 0.6831 (t) REVERT: C 14 ARG cc_start: 0.8088 (mtt90) cc_final: 0.6485 (tpt90) REVERT: D 18 GLN cc_start: 0.7262 (mt0) cc_final: 0.6918 (mt0) REVERT: D 25 SER cc_start: 0.8572 (t) cc_final: 0.8151 (p) REVERT: B 14 ARG cc_start: 0.8061 (mtt90) cc_final: 0.6482 (tpt90) REVERT: E 3 ARG cc_start: 0.5011 (mtt180) cc_final: 0.4541 (mmp-170) REVERT: E 11 ARG cc_start: 0.4178 (tpp-160) cc_final: 0.3460 (tpp-160) REVERT: E 12 MET cc_start: 0.7661 (ttm) cc_final: 0.7454 (ttm) REVERT: F 13 ASP cc_start: 0.7574 (p0) cc_final: 0.6985 (p0) REVERT: G 11 ARG cc_start: 0.7169 (mmm-85) cc_final: 0.5758 (tpm170) REVERT: G 14 ARG cc_start: 0.7885 (mtt90) cc_final: 0.6053 (ttp-170) REVERT: H 4 ARG cc_start: 0.7378 (mtp85) cc_final: 0.6350 (tmt-80) REVERT: H 15 ILE cc_start: 0.8588 (mm) cc_final: 0.8099 (mm) REVERT: H 19 SER cc_start: 0.8602 (m) cc_final: 0.8249 (p) REVERT: I 3 ARG cc_start: 0.6449 (ttm-80) cc_final: 0.5762 (mtp180) REVERT: I 5 SER cc_start: 0.7313 (m) cc_final: 0.6365 (p) REVERT: K 12 MET cc_start: 0.7136 (mtp) cc_final: 0.6818 (mpp) REVERT: M 3 ARG cc_start: 0.6428 (mtt180) cc_final: 0.4686 (ppt170) REVERT: M 11 ARG cc_start: 0.7250 (mmm-85) cc_final: 0.6398 (ttp-110) REVERT: M 27 ARG cc_start: 0.7331 (ttm110) cc_final: 0.6112 (mmp80) REVERT: N 13 ASP cc_start: 0.8042 (p0) cc_final: 0.7416 (p0) REVERT: N 15 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8769 (mt) REVERT: O 14 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7927 (mtm-85) REVERT: P 15 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8452 (mm) REVERT: R 24 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8203 (p0) REVERT: R 27 ARG cc_start: 0.7812 (ttt90) cc_final: 0.7320 (tmt170) REVERT: T 27 ARG cc_start: 0.7439 (ttt90) cc_final: 0.6828 (mtt-85) outliers start: 28 outliers final: 22 residues processed: 118 average time/residue: 0.1111 time to fit residues: 14.8566 Evaluate side-chains 121 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain Q residue 24 ASN Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain S residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 0.0570 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 ASN ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.178641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.164911 restraints weight = 4436.491| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 2.03 r_work: 0.4537 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4433 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4005 Z= 0.157 Angle : 0.650 6.084 5270 Z= 0.347 Chirality : 0.042 0.138 455 Planarity : 0.004 0.047 730 Dihedral : 7.782 74.814 632 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 7.09 % Allowed : 22.03 % Favored : 70.89 % 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: -5.63 (0.22), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.29 (0.17), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 11 TYR 0.011 0.001 TYR E 28 PHE 0.018 0.002 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3985) covalent geometry : angle 0.64089 ( 5230) SS BOND : bond 0.00290 ( 20) SS BOND : angle 1.41144 ( 40) hydrogen bonds : bond 0.01019 ( 5) hydrogen bonds : angle 5.45419 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7735 (m) cc_final: 0.6895 (t) REVERT: C 14 ARG cc_start: 0.8087 (mtt90) cc_final: 0.6536 (tpt90) REVERT: D 18 GLN cc_start: 0.7373 (mt0) cc_final: 0.7054 (mt0) REVERT: B 14 ARG cc_start: 0.8069 (mtt90) cc_final: 0.6524 (tpt90) REVERT: E 3 ARG cc_start: 0.5046 (mtt180) cc_final: 0.4614 (mmp-170) REVERT: E 11 ARG cc_start: 0.4320 (tpp-160) cc_final: 0.3632 (tpp-160) REVERT: E 12 MET cc_start: 0.7676 (ttm) cc_final: 0.7431 (ttm) REVERT: F 13 ASP cc_start: 0.7556 (p0) cc_final: 0.6978 (p0) REVERT: G 11 ARG cc_start: 0.7167 (mmm-85) cc_final: 0.5792 (tpm170) REVERT: G 14 ARG cc_start: 0.7919 (mtt90) cc_final: 0.6107 (ttp-170) REVERT: H 4 ARG cc_start: 0.7341 (mtp85) cc_final: 0.6532 (tmt-80) REVERT: H 15 ILE cc_start: 0.8597 (mm) cc_final: 0.8112 (mm) REVERT: H 19 SER cc_start: 0.8678 (m) cc_final: 0.8305 (p) REVERT: I 3 ARG cc_start: 0.6473 (ttm-80) cc_final: 0.5775 (mtp180) REVERT: I 5 SER cc_start: 0.7333 (m) cc_final: 0.6387 (p) REVERT: K 12 MET cc_start: 0.7204 (mtp) cc_final: 0.6926 (mpp) REVERT: L 18 GLN cc_start: 0.7456 (mt0) cc_final: 0.7245 (mt0) REVERT: M 3 ARG cc_start: 0.6382 (mtt180) cc_final: 0.4669 (ppt170) REVERT: M 11 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6395 (ttp-110) REVERT: M 27 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6118 (mmp80) REVERT: N 13 ASP cc_start: 0.7925 (p0) cc_final: 0.7269 (p0) REVERT: N 15 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8774 (mt) REVERT: O 14 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7945 (mtm-85) REVERT: P 15 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8468 (mm) REVERT: R 24 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8197 (p0) REVERT: R 27 ARG cc_start: 0.7866 (ttt90) cc_final: 0.7407 (tmt170) REVERT: T 27 ARG cc_start: 0.7485 (ttt90) cc_final: 0.6860 (mtt-85) outliers start: 28 outliers final: 22 residues processed: 115 average time/residue: 0.1138 time to fit residues: 14.7695 Evaluate side-chains 120 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain S residue 7 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.168685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.154870 restraints weight = 4723.197| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 2.03 r_work: 0.4444 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4339 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4005 Z= 0.307 Angle : 0.828 5.457 5270 Z= 0.449 Chirality : 0.049 0.165 455 Planarity : 0.006 0.043 730 Dihedral : 8.822 85.276 632 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.42 % Favored : 79.58 % Rotamer: Outliers : 6.84 % Allowed : 22.03 % Favored : 71.14 % 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: -5.78 (0.22), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.40 (0.17), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 11 TYR 0.018 0.002 TYR E 28 PHE 0.019 0.003 PHE F 26 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 3985) covalent geometry : angle 0.81032 ( 5230) SS BOND : bond 0.00626 ( 20) SS BOND : angle 2.11828 ( 40) hydrogen bonds : bond 0.01088 ( 5) hydrogen bonds : angle 6.35379 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7852 (m) cc_final: 0.6980 (t) REVERT: D 18 GLN cc_start: 0.7582 (mt0) cc_final: 0.7103 (mt0) REVERT: D 25 SER cc_start: 0.8745 (t) cc_final: 0.8327 (p) REVERT: B 14 ARG cc_start: 0.8138 (mtt90) cc_final: 0.6572 (tpt90) REVERT: E 3 ARG cc_start: 0.5225 (mtt180) cc_final: 0.4788 (mmp-170) REVERT: E 12 MET cc_start: 0.7770 (ttm) cc_final: 0.7499 (ttm) REVERT: G 11 ARG cc_start: 0.7404 (mmm-85) cc_final: 0.5828 (tpm170) REVERT: I 3 ARG cc_start: 0.6506 (ttm-80) cc_final: 0.5809 (mtp180) REVERT: I 5 SER cc_start: 0.7544 (m) cc_final: 0.6579 (p) REVERT: K 12 MET cc_start: 0.7402 (mtp) cc_final: 0.6944 (mpp) REVERT: M 3 ARG cc_start: 0.6526 (mtt180) cc_final: 0.4730 (ptt90) REVERT: M 11 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.6309 (ttp-110) REVERT: M 27 ARG cc_start: 0.7312 (ttm110) cc_final: 0.5976 (mmp-170) REVERT: N 13 ASP cc_start: 0.8131 (p0) cc_final: 0.7426 (p0) REVERT: N 15 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8732 (mt) REVERT: O 14 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7989 (mtm-85) REVERT: P 4 ARG cc_start: 0.7554 (mtp180) cc_final: 0.7214 (mtt180) REVERT: P 15 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8566 (mm) REVERT: R 24 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8388 (p0) REVERT: R 27 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7461 (tmt170) REVERT: T 15 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8093 (mm) outliers start: 27 outliers final: 21 residues processed: 109 average time/residue: 0.0907 time to fit residues: 11.3532 Evaluate side-chains 112 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain Q residue 24 ASN Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain S residue 7 CYS Chi-restraints excluded: chain T residue 15 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN O 24 ASN ** P 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.174902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.161215 restraints weight = 4470.741| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 2.02 r_work: 0.4507 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4403 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4005 Z= 0.183 Angle : 0.704 6.558 5270 Z= 0.376 Chirality : 0.044 0.144 455 Planarity : 0.004 0.051 730 Dihedral : 8.519 89.306 632 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % Rotamer: Outliers : 6.84 % Allowed : 22.53 % Favored : 70.63 % 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: -5.70 (0.22), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.17), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 11 TYR 0.017 0.002 TYR E 28 PHE 0.018 0.002 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 3985) covalent geometry : angle 0.69203 ( 5230) SS BOND : bond 0.00363 ( 20) SS BOND : angle 1.62653 ( 40) hydrogen bonds : bond 0.01240 ( 5) hydrogen bonds : angle 5.92123 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 950 Ramachandran restraints generated. 475 Oldfield, 0 Emsley, 475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.7860 (m) cc_final: 0.7012 (t) REVERT: D 18 GLN cc_start: 0.7415 (mt0) cc_final: 0.7028 (mt0) REVERT: D 25 SER cc_start: 0.8676 (t) cc_final: 0.8275 (p) REVERT: B 14 ARG cc_start: 0.8133 (mtt90) cc_final: 0.6556 (tpt90) REVERT: E 3 ARG cc_start: 0.5074 (mtt180) cc_final: 0.4709 (mmp-170) REVERT: E 11 ARG cc_start: 0.4273 (tpp-160) cc_final: 0.3603 (tpp-160) REVERT: E 12 MET cc_start: 0.7653 (ttm) cc_final: 0.7408 (ttm) REVERT: G 11 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.5745 (tpm170) REVERT: I 3 ARG cc_start: 0.6472 (ttm-80) cc_final: 0.5754 (mtp180) REVERT: I 5 SER cc_start: 0.7341 (m) cc_final: 0.6365 (p) REVERT: K 12 MET cc_start: 0.7377 (mtp) cc_final: 0.6947 (mpp) REVERT: M 3 ARG cc_start: 0.6435 (mtt180) cc_final: 0.4639 (ppt170) REVERT: M 11 ARG cc_start: 0.7223 (mmm-85) cc_final: 0.6265 (ttp-110) REVERT: M 27 ARG cc_start: 0.7271 (ttm110) cc_final: 0.6037 (mmp80) REVERT: N 13 ASP cc_start: 0.8002 (p0) cc_final: 0.7295 (p0) REVERT: N 15 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8711 (mt) REVERT: O 14 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7954 (mtm-85) REVERT: P 4 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7141 (mtt180) REVERT: P 15 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8501 (mm) REVERT: R 24 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8372 (p0) REVERT: R 27 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7448 (tmt170) REVERT: T 15 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8034 (mm) REVERT: T 27 ARG cc_start: 0.7476 (ttt90) cc_final: 0.6845 (mtt-85) outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 0.0835 time to fit residues: 10.7751 Evaluate side-chains 113 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain G residue 7 CYS Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain M residue 7 CYS Chi-restraints excluded: chain M residue 24 ASN Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain Q residue 7 CYS Chi-restraints excluded: chain Q residue 24 ASN Chi-restraints excluded: chain R residue 24 ASN Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain S residue 7 CYS Chi-restraints excluded: chain T residue 15 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 ASN ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 ASN P 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.173207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.159430 restraints weight = 4544.359| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 2.02 r_work: 0.4487 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4382 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4005 Z= 0.221 Angle : 0.738 6.444 5270 Z= 0.397 Chirality : 0.045 0.146 455 Planarity : 0.005 0.049 730 Dihedral : 8.513 82.277 632 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.95 % Favored : 81.05 % Rotamer: Outliers : 7.34 % Allowed : 22.28 % Favored : 70.38 % 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: -5.73 (0.22), residues: 475 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.17), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 11 TYR 0.017 0.002 TYR E 28 PHE 0.017 0.002 PHE A 8 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 3985) covalent geometry : angle 0.72389 ( 5230) SS BOND : bond 0.00436 ( 20) SS BOND : angle 1.78858 ( 40) hydrogen bonds : bond 0.01229 ( 5) hydrogen bonds : angle 6.10440 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1041.50 seconds wall clock time: 18 minutes 29.25 seconds (1109.25 seconds total)