Starting phenix.real_space_refine on Wed Sep 17 02:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iah_52781/09_2025/9iah_52781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iah_52781/09_2025/9iah_52781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iah_52781/09_2025/9iah_52781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iah_52781/09_2025/9iah_52781.map" model { file = "/net/cci-nas-00/data/ceres_data/9iah_52781/09_2025/9iah_52781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iah_52781/09_2025/9iah_52781.cif" } resolution = 3.17 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= 0.005 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 10 5.16 5 C 810 2.51 5 N 195 2.21 5 O 245 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1260 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 252 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 252 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 252 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 252 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 252 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 0.26, per 1000 atoms: 0.21 Number of scatterers: 1260 At special positions: 0 Unit cell: (53.3, 49.4, 42.9, 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 10 16.00 O 245 8.00 N 195 7.00 C 810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 27.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 8 removed outlier: 6.317A pdb=" N ILE E 2 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLN D 5 " --> pdb=" O ILE E 2 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR E 4 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N MET D 7 " --> pdb=" O THR E 4 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR E 6 " --> pdb=" O MET D 7 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 2 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLN C 5 " --> pdb=" O ILE D 2 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR D 4 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N MET C 7 " --> pdb=" O THR D 4 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR D 6 " --> pdb=" O MET C 7 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 2 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN B 5 " --> pdb=" O ILE C 2 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR C 4 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N MET B 7 " --> pdb=" O THR C 4 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 6 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 2 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLN A 5 " --> pdb=" O ILE B 2 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR B 4 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N MET A 7 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR B 6 " --> pdb=" O MET A 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.241A pdb=" N ASP E 11 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP D 11 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP C 11 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 11 " --> pdb=" O ILE A 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 18 through 19 removed outlier: 6.508A pdb=" N THR E 18 " --> pdb=" O TRP D 19 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 18 " --> pdb=" O TRP C 19 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 18 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR B 18 " --> pdb=" O TRP A 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 25 Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 33 removed outlier: 6.402A pdb=" N ILE E 29 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU D 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU E 31 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE D 29 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU C 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 31 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 29 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU B 32 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 31 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE B 29 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU A 32 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 31 " --> pdb=" O LEU A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 8 hydrogen bonds defined for protein. 24 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: 0.09 Time building geometry restraints manager: 0.15 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: 340 1.33 - 1.45: 160 1.45 - 1.56: 750 1.56 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 1270 Sorted by residual: bond pdb=" CB ILE E 12 " pdb=" CG2 ILE E 12 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CB ILE A 12 " pdb=" CG2 ILE A 12 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB ILE D 12 " pdb=" CG2 ILE D 12 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CD GLN B 5 " pdb=" OE1 GLN B 5 " ideal model delta sigma weight residual 1.231 1.212 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CB ILE C 12 " pdb=" CG2 ILE C 12 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.60e-01 ... (remaining 1265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.80: 1378 0.80 - 1.61: 228 1.61 - 2.41: 91 2.41 - 3.21: 18 3.21 - 4.02: 5 Bond angle restraints: 1720 Sorted by residual: angle pdb=" N LYS A 14 " pdb=" CA LYS A 14 " pdb=" C LYS A 14 " ideal model delta sigma weight residual 111.74 114.11 -2.37 1.35e+00 5.49e-01 3.07e+00 angle pdb=" N LYS B 14 " pdb=" CA LYS B 14 " pdb=" C LYS B 14 " ideal model delta sigma weight residual 111.74 113.98 -2.24 1.35e+00 5.49e-01 2.74e+00 angle pdb=" N LYS D 14 " pdb=" CA LYS D 14 " pdb=" C LYS D 14 " ideal model delta sigma weight residual 111.74 113.97 -2.23 1.35e+00 5.49e-01 2.72e+00 angle pdb=" CA GLN D 5 " pdb=" CB GLN D 5 " pdb=" CG GLN D 5 " ideal model delta sigma weight residual 114.10 110.99 3.11 2.00e+00 2.50e-01 2.42e+00 angle pdb=" N LYS E 14 " pdb=" CA LYS E 14 " pdb=" C LYS E 14 " ideal model delta sigma weight residual 111.74 113.83 -2.09 1.35e+00 5.49e-01 2.39e+00 ... (remaining 1715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.19: 643 10.19 - 20.37: 83 20.37 - 30.56: 24 30.56 - 40.75: 5 40.75 - 50.93: 5 Dihedral angle restraints: 760 sinusoidal: 270 harmonic: 490 Sorted by residual: dihedral pdb=" CA SER D 21 " pdb=" C SER D 21 " pdb=" N LEU D 22 " pdb=" CA LEU D 22 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER C 21 " pdb=" C SER C 21 " pdb=" N LEU C 22 " pdb=" CA LEU C 22 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA SER A 21 " pdb=" C SER A 21 " pdb=" N LEU A 22 " pdb=" CA LEU A 22 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 97 0.027 - 0.054: 64 0.054 - 0.080: 32 0.080 - 0.107: 20 0.107 - 0.134: 12 Chirality restraints: 225 Sorted by residual: chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE D 2 " pdb=" N ILE D 2 " pdb=" C ILE D 2 " pdb=" CB ILE D 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE E 2 " pdb=" N ILE E 2 " pdb=" C ILE E 2 " pdb=" CB ILE E 2 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 222 not shown) Planarity restraints: 200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 19 " 0.003 2.00e-02 2.50e+03 5.93e-03 8.79e-01 pdb=" CG TRP B 19 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 19 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 19 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 19 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 19 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 19 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 19 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 19 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 19 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 19 " -0.002 2.00e-02 2.50e+03 5.78e-03 8.36e-01 pdb=" CG TRP E 19 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP E 19 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP E 19 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 19 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 19 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 19 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 19 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 19 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 19 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 19 " 0.002 2.00e-02 2.50e+03 4.84e-03 5.85e-01 pdb=" CG TRP D 19 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP D 19 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP D 19 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 19 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 19 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 19 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 19 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 19 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 197 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 658 2.98 - 3.46: 1025 3.46 - 3.94: 2071 3.94 - 4.42: 2190 4.42 - 4.90: 4306 Nonbonded interactions: 10250 Sorted by model distance: nonbonded pdb=" O SER D 27 " pdb=" OG SER C 27 " model vdw 2.501 3.040 nonbonded pdb=" NE1 TRP C 19 " pdb=" O SER C 21 " model vdw 2.525 3.120 nonbonded pdb=" O SER C 27 " pdb=" OG SER B 27 " model vdw 2.540 3.040 nonbonded pdb=" O SER B 27 " pdb=" OG SER A 27 " model vdw 2.550 3.040 nonbonded pdb=" NE1 TRP A 19 " pdb=" O SER A 21 " model vdw 2.567 3.120 ... (remaining 10245 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: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' selection = chain 'A' } 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: 0.440 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.008 0.036 1270 Z= 0.345 Angle : 0.781 4.015 1720 Z= 0.423 Chirality : 0.052 0.134 225 Planarity : 0.002 0.007 200 Dihedral : 11.662 50.935 440 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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 aren not related in a simple way. whole: -1.94 (0.55), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR D 20 TRP 0.015 0.003 TRP B 19 Details of bonding type rmsd covalent geometry : bond 0.00818 ( 1270) covalent geometry : angle 0.78104 ( 1720) hydrogen bonds : bond 0.14036 ( 8) hydrogen bonds : angle 4.48371 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.025 Fit side-chains REVERT: E 14 LYS cc_start: 0.8871 (mttt) cc_final: 0.8630 (mtmt) REVERT: C 30 SER cc_start: 0.8795 (t) cc_final: 0.8425 (m) REVERT: B 13 GLN cc_start: 0.8270 (tt0) cc_final: 0.8012 (tt0) REVERT: B 24 MET cc_start: 0.9020 (mtp) cc_final: 0.8707 (mtt) REVERT: A 14 LYS cc_start: 0.8795 (mttt) cc_final: 0.8565 (mtmt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0729 time to fit residues: 1.8194 Evaluate side-chains 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081217 restraints weight = 1465.095| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.10 r_work: 0.3126 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1270 Z= 0.133 Angle : 0.518 3.165 1720 Z= 0.278 Chirality : 0.045 0.125 225 Planarity : 0.001 0.005 200 Dihedral : 6.318 20.295 170 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.74 % Allowed : 5.19 % Favored : 94.07 % 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 aren not related in a simple way. whole: -2.19 (0.56), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 20 TRP 0.005 0.001 TRP D 19 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 1270) covalent geometry : angle 0.51778 ( 1720) hydrogen bonds : bond 0.02023 ( 8) hydrogen bonds : angle 2.69751 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.065 Fit side-chains REVERT: E 14 LYS cc_start: 0.8721 (mttt) cc_final: 0.8521 (mtmt) REVERT: C 30 SER cc_start: 0.8659 (t) cc_final: 0.8199 (m) REVERT: B 24 MET cc_start: 0.8872 (mtp) cc_final: 0.8567 (mtt) REVERT: A 14 LYS cc_start: 0.8690 (mttt) cc_final: 0.8429 (mtmt) REVERT: A 24 MET cc_start: 0.9173 (mtp) cc_final: 0.8930 (mtm) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0498 time to fit residues: 1.2037 Evaluate side-chains 21 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN A 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075275 restraints weight = 1498.997| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.10 r_work: 0.2986 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1270 Z= 0.193 Angle : 0.553 3.778 1720 Z= 0.290 Chirality : 0.045 0.124 225 Planarity : 0.001 0.006 200 Dihedral : 6.123 20.889 170 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 8.15 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.56), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 20 TRP 0.007 0.001 TRP D 19 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 1270) covalent geometry : angle 0.55311 ( 1720) hydrogen bonds : bond 0.01613 ( 8) hydrogen bonds : angle 3.41477 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.025 Fit side-chains REVERT: E 14 LYS cc_start: 0.8672 (mttt) cc_final: 0.8400 (mtmt) REVERT: C 30 SER cc_start: 0.8653 (t) cc_final: 0.8187 (m) REVERT: B 24 MET cc_start: 0.8930 (mtp) cc_final: 0.8621 (mtt) REVERT: A 14 LYS cc_start: 0.8687 (mttt) cc_final: 0.8373 (mtmt) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0487 time to fit residues: 0.9829 Evaluate side-chains 18 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080301 restraints weight = 1514.806| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.16 r_work: 0.3080 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1270 Z= 0.113 Angle : 0.463 3.448 1720 Z= 0.243 Chirality : 0.044 0.119 225 Planarity : 0.001 0.004 200 Dihedral : 5.300 18.742 170 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.48 % Allowed : 8.15 % Favored : 90.37 % 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 aren not related in a simple way. whole: -2.42 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 20 TRP 0.003 0.001 TRP D 19 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 1270) covalent geometry : angle 0.46327 ( 1720) hydrogen bonds : bond 0.01227 ( 8) hydrogen bonds : angle 3.75113 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.030 Fit side-chains REVERT: E 14 LYS cc_start: 0.8637 (mttt) cc_final: 0.8324 (mtmt) REVERT: C 30 SER cc_start: 0.8648 (t) cc_final: 0.8201 (m) REVERT: A 14 LYS cc_start: 0.8725 (mttt) cc_final: 0.8382 (mtmt) outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.0374 time to fit residues: 0.8130 Evaluate side-chains 19 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075215 restraints weight = 1515.656| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.16 r_work: 0.3103 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1270 Z= 0.112 Angle : 0.454 3.350 1720 Z= 0.238 Chirality : 0.044 0.119 225 Planarity : 0.001 0.005 200 Dihedral : 5.069 17.951 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.22 % Allowed : 7.41 % Favored : 90.37 % 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 aren not related in a simple way. whole: -2.41 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 20 TRP 0.003 0.001 TRP D 19 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 1270) covalent geometry : angle 0.45370 ( 1720) hydrogen bonds : bond 0.00984 ( 8) hydrogen bonds : angle 3.81923 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.044 Fit side-chains REVERT: E 14 LYS cc_start: 0.8609 (mttt) cc_final: 0.8293 (mtmt) REVERT: C 30 SER cc_start: 0.8653 (t) cc_final: 0.8220 (m) REVERT: A 14 LYS cc_start: 0.8710 (mttt) cc_final: 0.8328 (mtmt) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.0529 time to fit residues: 1.0957 Evaluate side-chains 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain B residue 7 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074879 restraints weight = 1498.415| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.15 r_work: 0.3105 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1270 Z= 0.120 Angle : 0.451 3.344 1720 Z= 0.236 Chirality : 0.044 0.119 225 Planarity : 0.001 0.005 200 Dihedral : 4.997 17.942 170 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.22 % Allowed : 8.15 % Favored : 89.63 % 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 aren not related in a simple way. whole: -2.44 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 20 TRP 0.004 0.001 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 1270) covalent geometry : angle 0.45057 ( 1720) hydrogen bonds : bond 0.00908 ( 8) hydrogen bonds : angle 3.85300 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.047 Fit side-chains REVERT: E 14 LYS cc_start: 0.8582 (mttt) cc_final: 0.8248 (mtmt) REVERT: C 30 SER cc_start: 0.8699 (t) cc_final: 0.8267 (m) REVERT: A 14 LYS cc_start: 0.8697 (mttt) cc_final: 0.8290 (mtmt) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.0674 time to fit residues: 1.3826 Evaluate side-chains 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain B residue 7 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.075149 restraints weight = 1495.371| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.15 r_work: 0.3100 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1270 Z= 0.110 Angle : 0.439 3.231 1720 Z= 0.230 Chirality : 0.044 0.118 225 Planarity : 0.001 0.005 200 Dihedral : 4.822 17.273 170 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.22 % Allowed : 8.15 % Favored : 89.63 % 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 aren not related in a simple way. whole: -2.43 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 20 TRP 0.003 0.001 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 1270) covalent geometry : angle 0.43856 ( 1720) hydrogen bonds : bond 0.00800 ( 8) hydrogen bonds : angle 3.87594 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.046 Fit side-chains REVERT: E 14 LYS cc_start: 0.8572 (mttt) cc_final: 0.8243 (mtmt) REVERT: C 30 SER cc_start: 0.8677 (t) cc_final: 0.8250 (m) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.0559 time to fit residues: 1.1150 Evaluate side-chains 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain A residue 7 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074906 restraints weight = 1508.172| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.16 r_work: 0.3043 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1270 Z= 0.118 Angle : 0.443 3.286 1720 Z= 0.231 Chirality : 0.044 0.118 225 Planarity : 0.001 0.005 200 Dihedral : 4.817 17.349 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.96 % Allowed : 7.41 % Favored : 89.63 % 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 aren not related in a simple way. whole: -2.44 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 20 TRP 0.004 0.001 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 1270) covalent geometry : angle 0.44341 ( 1720) hydrogen bonds : bond 0.00847 ( 8) hydrogen bonds : angle 3.84650 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.047 Fit side-chains REVERT: E 14 LYS cc_start: 0.8525 (mttt) cc_final: 0.8170 (mtmt) REVERT: C 30 SER cc_start: 0.8589 (t) cc_final: 0.8173 (m) outliers start: 4 outliers final: 3 residues processed: 16 average time/residue: 0.0438 time to fit residues: 0.8589 Evaluate side-chains 19 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain A residue 7 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.0770 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077019 restraints weight = 1461.234| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.14 r_work: 0.3132 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1270 Z= 0.084 Angle : 0.413 3.162 1720 Z= 0.215 Chirality : 0.043 0.116 225 Planarity : 0.001 0.005 200 Dihedral : 4.420 16.099 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.22 % Allowed : 8.15 % Favored : 89.63 % 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 aren not related in a simple way. whole: -2.36 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 20 TRP 0.002 0.001 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 1270) covalent geometry : angle 0.41311 ( 1720) hydrogen bonds : bond 0.00949 ( 8) hydrogen bonds : angle 3.81656 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.050 Fit side-chains REVERT: E 14 LYS cc_start: 0.8585 (mttt) cc_final: 0.8230 (mtmt) REVERT: C 30 SER cc_start: 0.8654 (t) cc_final: 0.8266 (m) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.0471 time to fit residues: 0.9877 Evaluate side-chains 18 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain A residue 7 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074392 restraints weight = 1505.579| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.15 r_work: 0.3088 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1270 Z= 0.138 Angle : 0.459 3.463 1720 Z= 0.238 Chirality : 0.044 0.119 225 Planarity : 0.001 0.006 200 Dihedral : 4.729 14.702 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.22 % Allowed : 8.89 % Favored : 88.89 % 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 aren not related in a simple way. whole: -2.44 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 20 TRP 0.005 0.001 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 1270) covalent geometry : angle 0.45906 ( 1720) hydrogen bonds : bond 0.00831 ( 8) hydrogen bonds : angle 3.80507 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.047 Fit side-chains REVERT: E 14 LYS cc_start: 0.8588 (mttt) cc_final: 0.8194 (mtmt) REVERT: C 30 SER cc_start: 0.8678 (t) cc_final: 0.8287 (m) outliers start: 3 outliers final: 2 residues processed: 15 average time/residue: 0.0479 time to fit residues: 0.8762 Evaluate side-chains 17 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain A residue 7 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.090412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075140 restraints weight = 1502.584| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.20 r_work: 0.3031 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1270 Z= 0.108 Angle : 0.437 3.119 1720 Z= 0.228 Chirality : 0.044 0.118 225 Planarity : 0.001 0.006 200 Dihedral : 4.540 13.674 170 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.48 % Allowed : 9.63 % Favored : 88.89 % 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 aren not related in a simple way. whole: -2.41 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 20 TRP 0.004 0.001 TRP A 19 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 1270) covalent geometry : angle 0.43699 ( 1720) hydrogen bonds : bond 0.00758 ( 8) hydrogen bonds : angle 3.86288 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 543.75 seconds wall clock time: 10 minutes 14.47 seconds (614.47 seconds total)