Starting phenix.real_space_refine on Fri May 9 12:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iah_52781/05_2025/9iah_52781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iah_52781/05_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_52781/05_2025/9iah_52781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iah_52781/05_2025/9iah_52781.map" model { file = "/net/cci-nas-00/data/ceres_data/9iah_52781/05_2025/9iah_52781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iah_52781/05_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-5687/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: 1.12, per 1000 atoms: 0.89 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: 0.28 Conformation dependent library (CDL) restraints added in 458.1 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: 0.25 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: 0.31 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: 0.500 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.840 Find NCS groups from input model: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- 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 : 0.147 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: 0.1883 time to fit residues: 4.8200 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 : 0.129 ------------------------------------------------------------------------------- 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 = 37)----------------| | 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: 0.3134 rms_B_bonded: 2.28 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: 0.8038 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 : 0.146 Fit side-chains REVERT: C 30 SER cc_start: 0.8652 (t) cc_final: 0.8190 (m) REVERT: B 24 MET cc_start: 0.8851 (mtp) cc_final: 0.8558 (mtt) REVERT: A 14 LYS cc_start: 0.8677 (mttt) cc_final: 0.8422 (mtmt) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1790 time to fit residues: 4.3955 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=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: 0.7980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.097007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081751 restraints weight = 1453.227| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.15 r_work: 0.3088 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1876 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= 0.117 Angle : 0.479 3.426 1720 Z= 0.253 Chirality : 0.044 0.121 225 Planarity : 0.001 0.005 200 Dihedral : 5.540 18.754 170 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.86 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 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 19 TYR 0.004 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01516 ( 8) hydrogen bonds : angle 3.43340 ( 24) covalent geometry : bond 0.00271 ( 1270) covalent geometry : angle 0.47879 ( 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 : 0.128 Fit side-chains REVERT: D 30 SER cc_start: 0.9071 (t) cc_final: 0.8455 (m) REVERT: C 30 SER cc_start: 0.8652 (t) cc_final: 0.8204 (m) REVERT: A 14 LYS cc_start: 0.8689 (mttt) cc_final: 0.8408 (mtmt) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1429 time to fit residues: 3.1276 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 : 0.121 ------------------------------------------------------------------------------- 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: 4.9990 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.098792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083906 restraints weight = 1452.046| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.14 r_work: 0.3183 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1270 Z= 0.078 Angle : 0.426 3.094 1720 Z= 0.225 Chirality : 0.044 0.121 225 Planarity : 0.001 0.005 200 Dihedral : 4.706 16.305 170 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % 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 (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: -2.28 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 19 TYR 0.003 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01225 ( 8) hydrogen bonds : angle 3.69296 ( 24) covalent geometry : bond 0.00181 ( 1270) covalent geometry : angle 0.42605 ( 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 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.137 Fit side-chains REVERT: C 30 SER cc_start: 0.8597 (t) cc_final: 0.8184 (m) REVERT: A 14 LYS cc_start: 0.8701 (mttt) cc_final: 0.8303 (mtmt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1408 time to fit residues: 3.2499 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 : 0.150 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.091714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077075 restraints weight = 1459.371| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.11 r_work: 0.3157 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2348 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= 0.085 Angle : 0.427 3.417 1720 Z= 0.223 Chirality : 0.043 0.118 225 Planarity : 0.001 0.007 200 Dihedral : 4.551 13.308 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.63 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: -2.22 (0.59), 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 0.003 0.001 TRP A 19 TYR 0.004 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01029 ( 8) hydrogen bonds : angle 3.74161 ( 24) covalent geometry : bond 0.00194 ( 1270) covalent geometry : angle 0.42686 ( 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 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.138 Fit side-chains REVERT: C 30 SER cc_start: 0.8648 (t) cc_final: 0.8243 (m) REVERT: A 14 LYS cc_start: 0.8725 (mttt) cc_final: 0.8315 (mtmt) outliers start: 2 outliers final: 0 residues processed: 18 average time/residue: 0.1462 time to fit residues: 3.0583 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 12 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.095679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080584 restraints weight = 1480.080| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.16 r_work: 0.3087 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2368 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= 0.102 Angle : 0.435 3.250 1720 Z= 0.227 Chirality : 0.043 0.118 225 Planarity : 0.001 0.007 200 Dihedral : 4.603 13.744 170 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.22 % Allowed : 9.63 % 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: -2.30 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.45), 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 0.01015 ( 8) hydrogen bonds : angle 3.74924 ( 24) covalent geometry : bond 0.00231 ( 1270) covalent geometry : angle 0.43514 ( 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 20 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.138 Fit side-chains REVERT: C 30 SER cc_start: 0.8627 (t) cc_final: 0.8226 (m) REVERT: A 14 LYS cc_start: 0.8690 (mttt) cc_final: 0.8277 (mtmt) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.1521 time to fit residues: 2.9903 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain D 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: 3.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.095808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080634 restraints weight = 1445.375| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.14 r_work: 0.3128 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2425 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= 0.105 Angle : 0.435 3.240 1720 Z= 0.226 Chirality : 0.044 0.118 225 Planarity : 0.001 0.007 200 Dihedral : 4.561 13.841 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.63 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: -2.31 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (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 0.01010 ( 8) hydrogen bonds : angle 3.79600 ( 24) covalent geometry : bond 0.00237 ( 1270) covalent geometry : angle 0.43513 ( 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 17 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.140 Fit side-chains REVERT: C 30 SER cc_start: 0.8579 (t) cc_final: 0.8194 (m) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.1333 time to fit residues: 2.4704 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain D 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: 0.9980 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.094039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079089 restraints weight = 1445.154| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.09 r_work: 0.3116 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2425 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= 0.121 Angle : 0.450 3.363 1720 Z= 0.233 Chirality : 0.044 0.118 225 Planarity : 0.001 0.007 200 Dihedral : 4.667 14.338 170 Min Nonbonded Distance : 2.635 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: -2.35 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (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 0.01044 ( 8) hydrogen bonds : angle 3.89897 ( 24) covalent geometry : bond 0.00272 ( 1270) covalent geometry : angle 0.44952 ( 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 17 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.142 Fit side-chains REVERT: C 30 SER cc_start: 0.8656 (t) cc_final: 0.8254 (m) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.1175 time to fit residues: 2.1795 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 : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain D 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: 3.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.090685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075739 restraints weight = 1504.582| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.15 r_work: 0.3125 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2512 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= 0.099 Angle : 0.428 3.082 1720 Z= 0.223 Chirality : 0.044 0.117 225 Planarity : 0.001 0.006 200 Dihedral : 4.472 13.628 170 Min Nonbonded Distance : 2.634 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: -2.33 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.44), 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 3.97646 ( 24) covalent geometry : bond 0.00221 ( 1270) covalent geometry : angle 0.42811 ( 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: 2 poor density : 15 time to evaluate : 0.147 Fit side-chains REVERT: C 30 SER cc_start: 0.8609 (t) cc_final: 0.8230 (m) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.1139 time to fit residues: 2.1151 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 : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain D 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: 3.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.095505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080204 restraints weight = 1446.473| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.15 r_work: 0.3064 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2496 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= 0.115 Angle : 0.441 3.280 1720 Z= 0.229 Chirality : 0.044 0.119 225 Planarity : 0.001 0.006 200 Dihedral : 4.557 14.010 170 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.48 % Allowed : 11.11 % Favored : 87.41 % 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: -2.37 (0.58), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 TYR 0.004 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.00960 ( 8) hydrogen bonds : angle 3.97058 ( 24) covalent geometry : bond 0.00257 ( 1270) covalent geometry : angle 0.44127 ( 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: 2 poor density : 15 time to evaluate : 0.139 Fit side-chains REVERT: C 30 SER cc_start: 0.8575 (t) cc_final: 0.8195 (m) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.1111 time to fit residues: 2.0529 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 : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain D 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: 3.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.092662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077934 restraints weight = 1510.582| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.11 r_work: 0.3143 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2691 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= 0.075 Angle : 0.407 3.041 1720 Z= 0.212 Chirality : 0.043 0.115 225 Planarity : 0.001 0.006 200 Dihedral : 4.155 12.994 170 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.48 % Allowed : 11.11 % Favored : 87.41 % 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 (0.59), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 TYR 0.004 0.001 TYR B 20 Details of bonding type rmsd hydrogen bonds : bond 0.01015 ( 8) hydrogen bonds : angle 3.93138 ( 24) covalent geometry : bond 0.00169 ( 1270) covalent geometry : angle 0.40708 ( 1720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1185.60 seconds wall clock time: 21 minutes 15.53 seconds (1275.53 seconds total)