Starting phenix.real_space_refine on Sat Apr 26 14:59:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iah_52781/04_2025/9iah_52781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iah_52781/04_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_52781/04_2025/9iah_52781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iah_52781/04_2025/9iah_52781.map" model { file = "/net/cci-nas-00/data/ceres_data/9iah_52781/04_2025/9iah_52781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iah_52781/04_2025/9iah_52781.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 1.90, per 1000 atoms: 1.51 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: 0.29 Conformation dependent library (CDL) restraints added in 434.5 milliseconds 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: 0.19 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: 0.23 Time building geometry restraints manager: 0.35 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.330 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.040 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.003 TRP B 19 TYR 0.010 0.003 TYR D 20 Details of bonding type rmsd hydrogen bonds : bond 0.14036 ( 8) hydrogen bonds : angle 4.48371 ( 24) covalent geometry : bond 0.00818 ( 1270) covalent geometry : angle 0.78104 ( 1720) *********************** 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 : 0.138 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: 0.1855 time to fit residues: 4.7362 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.097544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082528 restraints weight = 1467.640| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.12 r_work: 0.3133 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1270 Z= 0.112 Angle : 0.504 3.326 1720 Z= 0.270 Chirality : 0.044 0.123 225 Planarity : 0.001 0.005 200 Dihedral : 6.084 19.940 170 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.56), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 19 TYR 0.003 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01604 ( 8) hydrogen bonds : angle 2.85075 ( 24) covalent geometry : bond 0.00260 ( 1270) covalent geometry : angle 0.50391 ( 1720) *********************** 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 : 0.137 Fit side-chains REVERT: C 30 SER cc_start: 0.8650 (t) cc_final: 0.8188 (m) REVERT: B 24 MET cc_start: 0.8849 (mtp) cc_final: 0.8555 (mtt) REVERT: A 14 LYS cc_start: 0.8676 (mttt) cc_final: 0.8420 (mtmt) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1824 time to fit residues: 4.4682 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 : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 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 13 GLN B 13 GLN A 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.097364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.082449 restraints weight = 1451.803| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.13 r_work: 0.3147 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1270 Z= 0.097 Angle : 0.460 3.278 1720 Z= 0.243 Chirality : 0.044 0.122 225 Planarity : 0.001 0.005 200 Dihedral : 5.279 17.922 170 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 10.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 19 TYR 0.004 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01598 ( 8) hydrogen bonds : angle 3.55862 ( 24) covalent geometry : bond 0.00226 ( 1270) covalent geometry : angle 0.45977 ( 1720) *********************** 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 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.134 Fit side-chains REVERT: D 30 SER cc_start: 0.9064 (t) cc_final: 0.8458 (m) REVERT: C 30 SER cc_start: 0.8637 (t) cc_final: 0.8195 (m) REVERT: A 14 LYS cc_start: 0.8682 (mttt) cc_final: 0.8395 (mtmt) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1431 time to fit residues: 3.1393 Evaluate side-chains 19 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.094621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079754 restraints weight = 1476.867| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.16 r_work: 0.3079 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1270 Z= 0.148 Angle : 0.491 3.537 1720 Z= 0.258 Chirality : 0.044 0.121 225 Planarity : 0.001 0.005 200 Dihedral : 5.416 18.890 170 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 19 TYR 0.006 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01186 ( 8) hydrogen bonds : angle 3.67218 ( 24) covalent geometry : bond 0.00339 ( 1270) covalent geometry : angle 0.49108 ( 1720) *********************** 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 19 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.136 Fit side-chains REVERT: C 30 SER cc_start: 0.8612 (t) cc_final: 0.8181 (m) REVERT: A 14 LYS cc_start: 0.8696 (mttt) cc_final: 0.8377 (mtmt) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.1451 time to fit residues: 3.0218 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 : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.0010 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.097522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082673 restraints weight = 1441.754| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.12 r_work: 0.3167 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1270 Z= 0.084 Angle : 0.424 3.196 1720 Z= 0.223 Chirality : 0.043 0.117 225 Planarity : 0.001 0.005 200 Dihedral : 4.700 16.829 170 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 : 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 19 TYR 0.004 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01102 ( 8) hydrogen bonds : angle 3.82646 ( 24) covalent geometry : bond 0.00192 ( 1270) covalent geometry : angle 0.42408 ( 1720) *********************** 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 22 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.145 Fit side-chains REVERT: C 30 SER cc_start: 0.8675 (t) cc_final: 0.8257 (m) REVERT: A 14 LYS cc_start: 0.8732 (mttt) cc_final: 0.8330 (mtmt) outliers start: 3 outliers final: 1 residues processed: 19 average time/residue: 0.1724 time to fit residues: 3.7171 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 : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.089771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074973 restraints weight = 1526.632| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.19 r_work: 0.3109 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2283 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= 0.124 Angle : 0.453 3.429 1720 Z= 0.237 Chirality : 0.044 0.119 225 Planarity : 0.001 0.007 200 Dihedral : 4.835 14.456 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.48 % Allowed : 10.37 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP A 19 TYR 0.005 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.00906 ( 8) hydrogen bonds : angle 3.90290 ( 24) covalent geometry : bond 0.00279 ( 1270) covalent geometry : angle 0.45339 ( 1720) *********************** 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 19 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.131 Fit side-chains REVERT: C 30 SER cc_start: 0.8699 (t) cc_final: 0.8286 (m) REVERT: A 14 LYS cc_start: 0.8703 (mttt) cc_final: 0.8302 (mtmt) outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.1491 time to fit residues: 2.9273 Evaluate side-chains 18 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077716 restraints weight = 1477.386| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.06 r_work: 0.3074 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1270 Z= 0.113 Angle : 0.440 3.235 1720 Z= 0.229 Chirality : 0.044 0.118 225 Planarity : 0.001 0.006 200 Dihedral : 4.703 13.931 170 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 : 1.48 % Allowed : 10.37 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 TYR 0.005 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.00968 ( 8) hydrogen bonds : angle 4.00832 ( 24) covalent geometry : bond 0.00255 ( 1270) covalent geometry : angle 0.43973 ( 1720) *********************** 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 18 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.135 Fit side-chains REVERT: C 30 SER cc_start: 0.8662 (t) cc_final: 0.8246 (m) outliers start: 2 outliers final: 1 residues processed: 16 average time/residue: 0.1290 time to fit residues: 2.4541 Evaluate side-chains 17 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.090962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.076422 restraints weight = 1469.174| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.08 r_work: 0.3046 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2314 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= 0.155 Angle : 0.478 3.633 1720 Z= 0.247 Chirality : 0.044 0.118 225 Planarity : 0.001 0.006 200 Dihedral : 4.963 15.355 170 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.74 % Allowed : 11.11 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.56), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 TYR 0.005 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01117 ( 8) hydrogen bonds : angle 4.03480 ( 24) covalent geometry : bond 0.00349 ( 1270) covalent geometry : angle 0.47764 ( 1720) *********************** 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 18 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.141 Fit side-chains REVERT: C 30 SER cc_start: 0.8654 (t) cc_final: 0.8232 (m) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.1332 time to fit residues: 2.6799 Evaluate side-chains 17 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.096343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.081133 restraints weight = 1470.381| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.16 r_work: 0.3073 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1270 Z= 0.095 Angle : 0.428 3.162 1720 Z= 0.223 Chirality : 0.043 0.117 225 Planarity : 0.001 0.006 200 Dihedral : 4.501 14.210 170 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.74 % Allowed : 11.11 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.57), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 TYR 0.005 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.00946 ( 8) hydrogen bonds : angle 4.09461 ( 24) covalent geometry : bond 0.00214 ( 1270) covalent geometry : angle 0.42753 ( 1720) *********************** 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 17 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.125 Fit side-chains REVERT: C 30 SER cc_start: 0.8589 (t) cc_final: 0.8189 (m) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0992 time to fit residues: 1.9633 Evaluate side-chains 16 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.088124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073637 restraints weight = 1518.175| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.10 r_work: 0.3019 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1270 Z= 0.173 Angle : 0.493 3.786 1720 Z= 0.255 Chirality : 0.044 0.118 225 Planarity : 0.001 0.006 200 Dihedral : 5.017 15.766 170 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.74 % Allowed : 11.11 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.54), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 TYR 0.005 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01139 ( 8) hydrogen bonds : angle 4.06013 ( 24) covalent geometry : bond 0.00389 ( 1270) covalent geometry : angle 0.49317 ( 1720) ********************** 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 17 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.140 Fit side-chains REVERT: C 30 SER cc_start: 0.8648 (t) cc_final: 0.8230 (m) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1092 time to fit residues: 2.1538 Evaluate side-chains 16 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.089300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074497 restraints weight = 1536.547| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.14 r_work: 0.3103 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2464 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= 0.116 Angle : 0.446 3.120 1720 Z= 0.232 Chirality : 0.044 0.117 225 Planarity : 0.001 0.006 200 Dihedral : 4.681 14.944 170 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.48 % Allowed : 10.37 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.55), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 TYR 0.005 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.00944 ( 8) hydrogen bonds : angle 4.15303 ( 24) covalent geometry : bond 0.00261 ( 1270) covalent geometry : angle 0.44572 ( 1720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1208.85 seconds wall clock time: 21 minutes 42.35 seconds (1302.35 seconds total)