Starting phenix.real_space_refine on Tue Feb 11 11:57:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ff2_29036/02_2025/8ff2_29036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ff2_29036/02_2025/8ff2_29036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ff2_29036/02_2025/8ff2_29036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ff2_29036/02_2025/8ff2_29036.map" model { file = "/net/cci-nas-00/data/ceres_data/8ff2_29036/02_2025/8ff2_29036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ff2_29036/02_2025/8ff2_29036.cif" } resolution = 2.87 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= 0.001 sd= 0.018 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 1840 2.51 5 N 510 2.21 5 O 550 1.98 5 H 2740 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5650 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 565 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 37} Restraints were copied for chains: C, B, E, D, G, F, I, K, J Time building chain proxies: 5.02, per 1000 atoms: 0.89 Number of scatterers: 5650 At special positions: 0 Unit cell: (70.56, 90.72, 47.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 550 8.00 N 510 7.00 C 1840 6.00 H 2740 1.00 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: 1.42 Conformation dependent library (CDL) restraints added in 380.8 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 640 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.728A pdb=" N GLN A 15 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL C 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE C 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 19 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN C 15 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL E 18 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE E 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 19 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL G 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE G 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE E 19 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN G 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL J 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU G 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE J 20 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE G 19 " --> pdb=" O PHE J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 21 removed outlier: 6.728A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL D 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE D 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 19 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL F 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE F 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE D 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN F 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL I 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU F 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE I 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 19 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN I 15 " --> pdb=" O LYS K 16 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL K 18 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU I 17 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE K 20 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE I 19 " --> pdb=" O PHE K 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 16 hydrogen bonds defined for protein. 48 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: 1.86 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2740 1.03 - 1.22: 0 1.22 - 1.42: 1360 1.42 - 1.61: 1590 1.61 - 1.80: 20 Bond restraints: 5710 Sorted by residual: bond pdb=" CA HIS G 6 " pdb=" C HIS G 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 8.17e-01 bond pdb=" CA HIS D 6 " pdb=" C HIS D 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 8.09e-01 bond pdb=" CA HIS K 6 " pdb=" C HIS K 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.98e-01 bond pdb=" CA HIS A 6 " pdb=" C HIS A 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.70e-01 bond pdb=" CA HIS C 6 " pdb=" C HIS C 6 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.51e-01 ... (remaining 5705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.48: 7927 0.48 - 0.96: 1769 0.96 - 1.44: 446 1.44 - 1.91: 51 1.91 - 2.39: 27 Bond angle restraints: 10220 Sorted by residual: angle pdb=" N GLY D 9 " pdb=" CA GLY D 9 " pdb=" C GLY D 9 " ideal model delta sigma weight residual 112.57 110.63 1.94 1.37e+00 5.33e-01 2.00e+00 angle pdb=" N GLY B 9 " pdb=" CA GLY B 9 " pdb=" C GLY B 9 " ideal model delta sigma weight residual 112.57 110.64 1.93 1.37e+00 5.33e-01 1.98e+00 angle pdb=" N GLY J 9 " pdb=" CA GLY J 9 " pdb=" C GLY J 9 " ideal model delta sigma weight residual 112.57 110.67 1.90 1.37e+00 5.33e-01 1.92e+00 angle pdb=" N GLY K 9 " pdb=" CA GLY K 9 " pdb=" C GLY K 9 " ideal model delta sigma weight residual 112.57 110.68 1.89 1.37e+00 5.33e-01 1.90e+00 angle pdb=" N GLY I 9 " pdb=" CA GLY I 9 " pdb=" C GLY I 9 " ideal model delta sigma weight residual 112.57 110.68 1.89 1.37e+00 5.33e-01 1.90e+00 ... (remaining 10215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.32: 2300 11.32 - 22.65: 200 22.65 - 33.97: 30 33.97 - 45.29: 60 45.29 - 56.61: 60 Dihedral angle restraints: 2650 sinusoidal: 1350 harmonic: 1300 Sorted by residual: dihedral pdb=" CA HIS K 13 " pdb=" C HIS K 13 " pdb=" N HIS K 14 " pdb=" CA HIS K 14 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS I 13 " pdb=" C HIS I 13 " pdb=" N HIS I 14 " pdb=" CA HIS I 14 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS A 13 " pdb=" C HIS A 13 " pdb=" N HIS A 14 " pdb=" CA HIS A 14 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 2647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 214 0.023 - 0.046: 126 0.046 - 0.069: 0 0.069 - 0.092: 10 0.092 - 0.115: 50 Chirality restraints: 400 Sorted by residual: chirality pdb=" CA VAL E 18 " pdb=" N VAL E 18 " pdb=" C VAL E 18 " pdb=" CB VAL E 18 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA VAL D 18 " pdb=" N VAL D 18 " pdb=" C VAL D 18 " pdb=" CB VAL D 18 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 chirality pdb=" CA VAL G 18 " pdb=" N VAL G 18 " pdb=" C VAL G 18 " pdb=" CB VAL G 18 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 397 not shown) Planarity restraints: 900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 13 " 0.004 2.00e-02 2.50e+03 3.40e-03 2.60e-01 pdb=" CG HIS A 13 " -0.009 2.00e-02 2.50e+03 pdb=" ND1 HIS A 13 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 13 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS A 13 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 13 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS A 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 13 " -0.005 2.00e-02 2.50e+03 3.35e-03 2.52e-01 pdb=" CG HIS K 13 " 0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS K 13 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 13 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS K 13 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS K 13 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS K 13 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS K 13 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS K 13 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 13 " 0.004 2.00e-02 2.50e+03 3.28e-03 2.43e-01 pdb=" CG HIS G 13 " -0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS G 13 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS G 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS G 13 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS G 13 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS G 13 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS G 13 " 0.001 2.00e-02 2.50e+03 ... (remaining 897 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.37: 2123 2.37 - 2.93: 12418 2.93 - 3.49: 13179 3.49 - 4.04: 20019 4.04 - 4.60: 28533 Nonbonded interactions: 76272 Sorted by model distance: nonbonded pdb="HE22 GLN A 15 " pdb=" O VAL D 36 " model vdw 1.818 2.450 nonbonded pdb="HE22 GLN E 15 " pdb=" O VAL I 36 " model vdw 1.818 2.450 nonbonded pdb="HE22 GLN B 15 " pdb=" O VAL E 36 " model vdw 1.818 2.450 nonbonded pdb="HE22 GLN G 15 " pdb=" O VAL K 36 " model vdw 1.818 2.450 nonbonded pdb="HE22 GLN F 15 " pdb=" O VAL J 36 " model vdw 1.818 2.450 ... (remaining 76267 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'J' } 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: 0.010 Normalize map: mean=0, sd=1: 6.380 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.570 Find NCS groups from input model: 0.090 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.005 0.017 2970 Z= 0.319 Angle : 0.429 1.979 3970 Z= 0.265 Chirality : 0.044 0.115 400 Planarity : 0.002 0.009 530 Dihedral : 10.635 42.562 1020 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.01 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 13 PHE 0.006 0.001 PHE D 19 TYR 0.001 0.001 TYR K 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.6486 (mmp-170) REVERT: A 27 ASN cc_start: 0.8497 (m-40) cc_final: 0.8264 (m110) REVERT: B 3 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7504 (tp30) REVERT: B 5 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.6673 (mmp-170) REVERT: C 5 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7657 (mtp85) REVERT: C 7 ASP cc_start: 0.8358 (m-30) cc_final: 0.8157 (m-30) REVERT: C 27 ASN cc_start: 0.8597 (m-40) cc_final: 0.8370 (m-40) REVERT: D 11 GLU cc_start: 0.8388 (pt0) cc_final: 0.8003 (pt0) REVERT: F 5 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8087 (tpp80) REVERT: F 13 HIS cc_start: 0.7885 (m90) cc_final: 0.7644 (m-70) REVERT: G 28 LYS cc_start: 0.8975 (tttt) cc_final: 0.8657 (tttm) REVERT: I 8 SER cc_start: 0.8898 (m) cc_final: 0.8548 (m) REVERT: I 11 GLU cc_start: 0.8275 (pt0) cc_final: 0.7988 (pt0) REVERT: I 28 LYS cc_start: 0.9122 (tttt) cc_final: 0.8849 (tttm) REVERT: J 5 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.5872 (ppt170) REVERT: J 28 LYS cc_start: 0.9081 (tttt) cc_final: 0.8160 (tppt) REVERT: K 5 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.6282 (pmt170) REVERT: K 11 GLU cc_start: 0.8203 (pt0) cc_final: 0.7920 (pt0) REVERT: K 28 LYS cc_start: 0.8996 (tttt) cc_final: 0.8220 (tppt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 2.2241 time to fit residues: 289.8356 Evaluate side-chains 108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.088741 restraints weight = 14190.578| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.46 r_work: 0.3516 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2970 Z= 0.370 Angle : 0.549 3.655 3970 Z= 0.319 Chirality : 0.051 0.152 400 Planarity : 0.002 0.010 530 Dihedral : 6.433 21.068 390 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.38 % Allowed : 16.55 % Favored : 82.07 % 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: -2.13 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 13 PHE 0.005 0.001 PHE J 19 TYR 0.013 0.001 TYR I 10 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.6772 (mmp-170) REVERT: A 28 LYS cc_start: 0.9274 (tttt) cc_final: 0.9002 (tttp) REVERT: B 3 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7921 (tp30) REVERT: B 5 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.7154 (mmp-170) REVERT: C 5 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8047 (mtp85) REVERT: D 11 GLU cc_start: 0.8287 (pt0) cc_final: 0.8006 (pt0) REVERT: F 5 ARG cc_start: 0.8599 (mtt-85) cc_final: 0.8356 (tpp80) REVERT: G 1 ASP cc_start: 0.7212 (p0) cc_final: 0.6808 (p0) REVERT: I 1 ASP cc_start: 0.7787 (p0) cc_final: 0.7514 (p0) REVERT: I 8 SER cc_start: 0.8866 (m) cc_final: 0.8263 (m) REVERT: I 11 GLU cc_start: 0.8453 (pt0) cc_final: 0.8002 (pt0) REVERT: I 28 LYS cc_start: 0.9231 (tttt) cc_final: 0.8959 (tttp) REVERT: J 5 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.6196 (ppt170) REVERT: J 8 SER cc_start: 0.9110 (m) cc_final: 0.8890 (t) REVERT: J 10 TYR cc_start: 0.8527 (t80) cc_final: 0.8309 (t80) REVERT: J 11 GLU cc_start: 0.8271 (pt0) cc_final: 0.7810 (mm-30) REVERT: J 28 LYS cc_start: 0.9235 (tttt) cc_final: 0.8359 (tppt) REVERT: K 5 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.6596 (pmt170) REVERT: K 28 LYS cc_start: 0.9153 (tttt) cc_final: 0.8374 (tppt) outliers start: 4 outliers final: 1 residues processed: 115 average time/residue: 2.4681 time to fit residues: 290.4759 Evaluate side-chains 109 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.095862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.088445 restraints weight = 14625.755| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.31 r_work: 0.3542 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2970 Z= 0.275 Angle : 0.476 3.534 3970 Z= 0.277 Chirality : 0.050 0.136 400 Planarity : 0.002 0.017 530 Dihedral : 6.089 19.983 390 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.07 % Allowed : 19.31 % Favored : 78.62 % 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 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 13 PHE 0.003 0.001 PHE J 19 TYR 0.011 0.001 TYR G 10 ARG 0.002 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.6792 (mmp-170) REVERT: A 28 LYS cc_start: 0.9284 (tttt) cc_final: 0.9068 (tttp) REVERT: B 5 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.7193 (mmp-170) REVERT: C 5 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.8040 (mtp85) REVERT: D 8 SER cc_start: 0.8873 (m) cc_final: 0.8666 (t) REVERT: E 1 ASP cc_start: 0.7664 (p0) cc_final: 0.7456 (p0) REVERT: E 28 LYS cc_start: 0.9132 (tttt) cc_final: 0.8774 (ttpt) REVERT: I 1 ASP cc_start: 0.7955 (p0) cc_final: 0.7573 (p0) REVERT: I 8 SER cc_start: 0.8831 (m) cc_final: 0.8109 (m) REVERT: I 11 GLU cc_start: 0.8286 (pt0) cc_final: 0.7859 (pt0) REVERT: I 28 LYS cc_start: 0.9283 (tttt) cc_final: 0.9016 (tttm) REVERT: J 5 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.6217 (ppt170) REVERT: J 10 TYR cc_start: 0.8545 (t80) cc_final: 0.7994 (t80) REVERT: J 11 GLU cc_start: 0.8149 (pt0) cc_final: 0.7849 (mm-30) REVERT: J 28 LYS cc_start: 0.9279 (tttt) cc_final: 0.8497 (tppt) REVERT: K 5 ARG cc_start: 0.8525 (mtt-85) cc_final: 0.6627 (pmt170) REVERT: K 28 LYS cc_start: 0.9159 (tttt) cc_final: 0.8488 (tppt) outliers start: 6 outliers final: 5 residues processed: 109 average time/residue: 2.4463 time to fit residues: 273.4276 Evaluate side-chains 111 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.093331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.085632 restraints weight = 15340.582| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.56 r_work: 0.3520 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2970 Z= 0.392 Angle : 0.513 3.723 3970 Z= 0.302 Chirality : 0.050 0.148 400 Planarity : 0.002 0.021 530 Dihedral : 6.301 21.019 390 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.10 % Allowed : 20.00 % Favored : 76.90 % 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: -2.45 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 13 PHE 0.005 0.001 PHE E 19 TYR 0.008 0.001 TYR D 10 ARG 0.002 0.001 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.6674 (mmp-170) REVERT: A 28 LYS cc_start: 0.9287 (tttt) cc_final: 0.9037 (tttp) REVERT: B 5 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.7123 (mmp-170) REVERT: C 5 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.8039 (mtp85) REVERT: E 1 ASP cc_start: 0.7802 (p0) cc_final: 0.7593 (p0) REVERT: E 8 SER cc_start: 0.8801 (m) cc_final: 0.8226 (t) REVERT: E 28 LYS cc_start: 0.9059 (tttt) cc_final: 0.8725 (ttpt) REVERT: F 15 GLN cc_start: 0.8625 (pt0) cc_final: 0.8421 (pt0) REVERT: F 23 ASP cc_start: 0.7760 (m-30) cc_final: 0.7545 (m-30) REVERT: I 1 ASP cc_start: 0.8148 (p0) cc_final: 0.7782 (p0) REVERT: I 8 SER cc_start: 0.8888 (m) cc_final: 0.8100 (m) REVERT: I 11 GLU cc_start: 0.8332 (pt0) cc_final: 0.7845 (pt0) REVERT: I 28 LYS cc_start: 0.9273 (tttt) cc_final: 0.8985 (tttp) REVERT: J 5 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.6184 (ppt170) REVERT: J 28 LYS cc_start: 0.9242 (tttt) cc_final: 0.8358 (tppt) REVERT: K 5 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.6551 (pmt170) REVERT: K 28 LYS cc_start: 0.9122 (tttt) cc_final: 0.8336 (tppt) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 2.3884 time to fit residues: 269.5709 Evaluate side-chains 113 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.093688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.085639 restraints weight = 15201.923| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.59 r_work: 0.3538 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2970 Z= 0.400 Angle : 0.546 4.309 3970 Z= 0.320 Chirality : 0.050 0.143 400 Planarity : 0.002 0.014 530 Dihedral : 6.318 20.050 390 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.10 % Allowed : 23.79 % Favored : 73.10 % 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: -2.64 (0.32), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.006 0.001 PHE I 4 TYR 0.013 0.002 TYR I 10 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.6676 (mmp-170) REVERT: A 28 LYS cc_start: 0.9301 (tttt) cc_final: 0.9052 (tttp) REVERT: B 5 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.7063 (mmp-170) REVERT: C 5 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8036 (mtp85) REVERT: E 8 SER cc_start: 0.8761 (m) cc_final: 0.8195 (t) REVERT: E 28 LYS cc_start: 0.9091 (tttt) cc_final: 0.8677 (ttpt) REVERT: F 3 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: I 1 ASP cc_start: 0.8137 (p0) cc_final: 0.7794 (p0) REVERT: I 8 SER cc_start: 0.8894 (m) cc_final: 0.8079 (m) REVERT: I 11 GLU cc_start: 0.8276 (pt0) cc_final: 0.7912 (pt0) REVERT: I 28 LYS cc_start: 0.9238 (tttt) cc_final: 0.8940 (tttp) REVERT: J 5 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.6201 (ppt170) REVERT: J 28 LYS cc_start: 0.9280 (tttt) cc_final: 0.8353 (tppt) REVERT: K 5 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.6612 (pmt170) REVERT: K 28 LYS cc_start: 0.9139 (tttt) cc_final: 0.8356 (tppt) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 2.3527 time to fit residues: 265.2687 Evaluate side-chains 114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.094829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.086520 restraints weight = 14926.623| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.64 r_work: 0.3566 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2970 Z= 0.307 Angle : 0.526 4.978 3970 Z= 0.304 Chirality : 0.050 0.141 400 Planarity : 0.002 0.017 530 Dihedral : 6.128 19.426 390 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.10 % Allowed : 27.24 % Favored : 69.66 % 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: -2.64 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.007 0.001 PHE A 4 TYR 0.013 0.002 TYR I 10 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.6660 (mmp-170) REVERT: A 28 LYS cc_start: 0.9305 (tttt) cc_final: 0.9063 (tttp) REVERT: B 5 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.6808 (mmp-170) REVERT: C 5 ARG cc_start: 0.8254 (mtt-85) cc_final: 0.7993 (mtp85) REVERT: E 8 SER cc_start: 0.8822 (m) cc_final: 0.8309 (t) REVERT: E 28 LYS cc_start: 0.9135 (tttt) cc_final: 0.8745 (ttpt) REVERT: F 3 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6978 (tm-30) REVERT: F 11 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: I 1 ASP cc_start: 0.8136 (p0) cc_final: 0.7784 (p0) REVERT: I 28 LYS cc_start: 0.9255 (tttt) cc_final: 0.8969 (tttm) REVERT: J 5 ARG cc_start: 0.8465 (mtt-85) cc_final: 0.6193 (ppt170) REVERT: J 28 LYS cc_start: 0.9299 (tttt) cc_final: 0.8388 (tppt) REVERT: K 3 GLU cc_start: 0.8241 (mp0) cc_final: 0.8035 (mp0) REVERT: K 5 ARG cc_start: 0.8660 (mtt-85) cc_final: 0.6636 (pmt170) REVERT: K 28 LYS cc_start: 0.9171 (tttt) cc_final: 0.8416 (tppt) outliers start: 9 outliers final: 7 residues processed: 108 average time/residue: 2.3420 time to fit residues: 259.1484 Evaluate side-chains 115 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 0.0980 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.095558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087341 restraints weight = 15096.602| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.65 r_work: 0.3591 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2970 Z= 0.242 Angle : 0.506 5.333 3970 Z= 0.290 Chirality : 0.050 0.138 400 Planarity : 0.002 0.017 530 Dihedral : 5.856 19.052 390 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.07 % Allowed : 29.66 % Favored : 68.28 % 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: -2.58 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 13 PHE 0.008 0.001 PHE I 4 TYR 0.012 0.002 TYR G 10 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.6769 (mmp-170) REVERT: A 28 LYS cc_start: 0.9294 (tttt) cc_final: 0.9060 (tttp) REVERT: B 5 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.6807 (mmp-170) REVERT: E 8 SER cc_start: 0.8736 (m) cc_final: 0.8178 (t) REVERT: E 11 GLU cc_start: 0.8274 (pt0) cc_final: 0.7851 (pt0) REVERT: E 28 LYS cc_start: 0.9140 (tttt) cc_final: 0.8782 (ttpt) REVERT: I 1 ASP cc_start: 0.8149 (p0) cc_final: 0.7774 (p0) REVERT: I 28 LYS cc_start: 0.9276 (tttt) cc_final: 0.8989 (tttm) REVERT: J 5 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.6193 (ppt170) REVERT: J 28 LYS cc_start: 0.9352 (tttt) cc_final: 0.8468 (tppt) REVERT: K 5 ARG cc_start: 0.8641 (mtt-85) cc_final: 0.6573 (pmt170) REVERT: K 28 LYS cc_start: 0.9159 (tttt) cc_final: 0.8400 (tppt) outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 2.2606 time to fit residues: 241.1885 Evaluate side-chains 108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.088316 restraints weight = 14655.809| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.67 r_work: 0.3595 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2970 Z= 0.259 Angle : 0.530 5.509 3970 Z= 0.302 Chirality : 0.050 0.135 400 Planarity : 0.002 0.013 530 Dihedral : 5.822 19.278 390 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.72 % Allowed : 31.38 % Favored : 66.90 % 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: -2.58 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.008 0.001 PHE I 4 TYR 0.012 0.001 TYR J 10 ARG 0.003 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.6651 (mmp-170) REVERT: A 28 LYS cc_start: 0.9297 (tttt) cc_final: 0.9056 (tttp) REVERT: B 5 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.6985 (mmp-170) REVERT: C 28 LYS cc_start: 0.9231 (tttp) cc_final: 0.8847 (ttmt) REVERT: E 3 GLU cc_start: 0.8226 (tt0) cc_final: 0.7610 (tm-30) REVERT: E 8 SER cc_start: 0.8725 (m) cc_final: 0.8164 (t) REVERT: E 11 GLU cc_start: 0.8287 (pt0) cc_final: 0.7861 (pt0) REVERT: E 28 LYS cc_start: 0.9142 (tttt) cc_final: 0.8776 (ttpt) REVERT: G 23 ASP cc_start: 0.7883 (m-30) cc_final: 0.7391 (m-30) REVERT: I 1 ASP cc_start: 0.8189 (p0) cc_final: 0.7801 (p0) REVERT: I 28 LYS cc_start: 0.9263 (tttt) cc_final: 0.8972 (tttp) REVERT: J 5 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.6191 (ppt170) REVERT: J 28 LYS cc_start: 0.9333 (tttt) cc_final: 0.8418 (tppt) REVERT: K 5 ARG cc_start: 0.8628 (mtt-85) cc_final: 0.6552 (pmt170) REVERT: K 28 LYS cc_start: 0.9150 (tttt) cc_final: 0.8384 (tppt) outliers start: 5 outliers final: 4 residues processed: 105 average time/residue: 2.2708 time to fit residues: 244.6591 Evaluate side-chains 108 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.097144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.088466 restraints weight = 14549.470| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.65 r_work: 0.3558 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2970 Z= 0.402 Angle : 0.559 4.954 3970 Z= 0.324 Chirality : 0.050 0.148 400 Planarity : 0.002 0.020 530 Dihedral : 6.088 20.144 390 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 32.41 % Favored : 65.52 % 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: -2.83 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.009 0.001 PHE I 4 TYR 0.008 0.001 TYR K 10 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8420 (mtt-85) cc_final: 0.6875 (mmp-170) REVERT: A 28 LYS cc_start: 0.9309 (tttt) cc_final: 0.9063 (tttp) REVERT: E 3 GLU cc_start: 0.8188 (tt0) cc_final: 0.7534 (tm-30) REVERT: E 8 SER cc_start: 0.8846 (m) cc_final: 0.8376 (t) REVERT: E 28 LYS cc_start: 0.9130 (tttt) cc_final: 0.8723 (ttpt) REVERT: F 4 PHE cc_start: 0.7950 (m-10) cc_final: 0.7689 (m-80) REVERT: F 8 SER cc_start: 0.8707 (m) cc_final: 0.8264 (t) REVERT: G 23 ASP cc_start: 0.7929 (m-30) cc_final: 0.7397 (m-30) REVERT: I 1 ASP cc_start: 0.8230 (p0) cc_final: 0.7843 (p0) REVERT: I 28 LYS cc_start: 0.9280 (tttt) cc_final: 0.8989 (tttp) REVERT: J 5 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.6228 (ppt170) REVERT: J 28 LYS cc_start: 0.9333 (tttt) cc_final: 0.8422 (tppt) REVERT: K 5 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.6624 (pmt170) REVERT: K 28 LYS cc_start: 0.9145 (tttt) cc_final: 0.8373 (tppt) outliers start: 6 outliers final: 5 residues processed: 107 average time/residue: 2.2075 time to fit residues: 243.6341 Evaluate side-chains 110 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.095730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.087543 restraints weight = 15162.085| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.67 r_work: 0.3588 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2970 Z= 0.273 Angle : 0.566 6.154 3970 Z= 0.322 Chirality : 0.050 0.135 400 Planarity : 0.002 0.012 530 Dihedral : 5.914 19.403 390 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.72 % Allowed : 33.45 % Favored : 64.83 % 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: -2.78 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 13 PHE 0.007 0.001 PHE I 4 TYR 0.012 0.002 TYR J 10 ARG 0.002 0.000 ARG D 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9304 (tttt) cc_final: 0.9047 (tttp) REVERT: B 5 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.6958 (mmp-170) REVERT: C 28 LYS cc_start: 0.9208 (tttp) cc_final: 0.8810 (ttmt) REVERT: E 3 GLU cc_start: 0.8267 (tt0) cc_final: 0.7577 (tm-30) REVERT: E 8 SER cc_start: 0.8733 (m) cc_final: 0.8254 (t) REVERT: E 28 LYS cc_start: 0.9139 (tttt) cc_final: 0.8776 (ttpt) REVERT: G 23 ASP cc_start: 0.7908 (m-30) cc_final: 0.7419 (m-30) REVERT: I 1 ASP cc_start: 0.8238 (p0) cc_final: 0.7821 (p0) REVERT: I 28 LYS cc_start: 0.9239 (tttt) cc_final: 0.8941 (tttp) REVERT: J 5 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.6177 (ppt170) REVERT: J 28 LYS cc_start: 0.9319 (tttt) cc_final: 0.8401 (tppt) REVERT: K 5 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.6492 (pmt170) REVERT: K 28 LYS cc_start: 0.9119 (tttt) cc_final: 0.8328 (tppt) outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 2.2435 time to fit residues: 237.3064 Evaluate side-chains 106 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.097151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.088395 restraints weight = 14617.248| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.66 r_work: 0.3573 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2970 Z= 0.376 Angle : 0.577 5.637 3970 Z= 0.332 Chirality : 0.050 0.136 400 Planarity : 0.002 0.017 530 Dihedral : 6.098 19.952 390 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 32.76 % Favored : 65.17 % 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: -2.97 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.009 0.001 PHE I 4 TYR 0.012 0.001 TYR I 10 ARG 0.001 0.000 ARG G 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6979.11 seconds wall clock time: 123 minutes 2.89 seconds (7382.89 seconds total)