Starting phenix.real_space_refine on Fri Dec 27 15:09:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ff2_29036/12_2024/8ff2_29036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ff2_29036/12_2024/8ff2_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_29036/12_2024/8ff2_29036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ff2_29036/12_2024/8ff2_29036.map" model { file = "/net/cci-nas-00/data/ceres_data/8ff2_29036/12_2024/8ff2_29036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ff2_29036/12_2024/8ff2_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-5532/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: 4.46, per 1000 atoms: 0.79 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: 1.19 Conformation dependent library (CDL) restraints added in 343.3 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: 0.52 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: 1.59 Time building geometry restraints manager: 1.47 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 7.050 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.130 Find NCS groups from input model: 0.160 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- 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 : 0.491 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: 2.1849 time to fit residues: 284.7211 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 : 0.476 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.6487 (mmp-170) REVERT: A 28 LYS cc_start: 0.9250 (tttt) cc_final: 0.8959 (tttp) REVERT: B 5 ARG cc_start: 0.8499 (mtt-85) cc_final: 0.6837 (mmp-170) REVERT: C 5 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.7894 (mtp85) REVERT: D 11 GLU cc_start: 0.8237 (pt0) cc_final: 0.7881 (pt0) REVERT: F 5 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.8230 (tpp80) REVERT: G 1 ASP cc_start: 0.7143 (p0) cc_final: 0.6696 (p0) REVERT: I 1 ASP cc_start: 0.7791 (p0) cc_final: 0.7574 (p0) REVERT: I 8 SER cc_start: 0.8826 (m) cc_final: 0.8248 (m) REVERT: I 11 GLU cc_start: 0.8406 (pt0) cc_final: 0.7976 (pt0) REVERT: I 28 LYS cc_start: 0.9147 (tttt) cc_final: 0.8839 (tttp) REVERT: J 5 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.6058 (ppt170) REVERT: J 8 SER cc_start: 0.9075 (m) cc_final: 0.8796 (t) REVERT: J 10 TYR cc_start: 0.8463 (t80) cc_final: 0.8220 (t80) REVERT: J 11 GLU cc_start: 0.8035 (pt0) cc_final: 0.7583 (mm-30) REVERT: J 28 LYS cc_start: 0.9124 (tttt) cc_final: 0.8202 (tppt) REVERT: K 5 ARG cc_start: 0.8656 (mtt-85) cc_final: 0.6382 (pmt170) REVERT: K 28 LYS cc_start: 0.9017 (tttt) cc_final: 0.8207 (tppt) outliers start: 4 outliers final: 1 residues processed: 115 average time/residue: 2.4492 time to fit residues: 288.2580 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 : 0.424 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2970 Z= 0.322 Angle : 0.493 3.559 3970 Z= 0.288 Chirality : 0.050 0.139 400 Planarity : 0.002 0.017 530 Dihedral : 6.205 20.178 390 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.41 % Allowed : 19.31 % Favored : 78.28 % 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: -2.25 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 13 PHE 0.004 0.001 PHE E 19 TYR 0.012 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 115 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8203 (mtt-85) cc_final: 0.6487 (mmp-170) REVERT: A 28 LYS cc_start: 0.9246 (tttt) cc_final: 0.8948 (tttp) REVERT: B 5 ARG cc_start: 0.8405 (mtt-85) cc_final: 0.6860 (mmp-170) REVERT: C 5 ARG cc_start: 0.8260 (mtt-85) cc_final: 0.7858 (mtp85) REVERT: D 8 SER cc_start: 0.8824 (m) cc_final: 0.8560 (t) REVERT: E 28 LYS cc_start: 0.9056 (tttt) cc_final: 0.8614 (ttpt) REVERT: F 11 GLU cc_start: 0.8343 (pt0) cc_final: 0.8107 (pt0) REVERT: I 1 ASP cc_start: 0.7941 (p0) cc_final: 0.7652 (p0) REVERT: I 8 SER cc_start: 0.8863 (m) cc_final: 0.7988 (m) REVERT: I 11 GLU cc_start: 0.8245 (pt0) cc_final: 0.7759 (pt0) REVERT: I 28 LYS cc_start: 0.9143 (tttt) cc_final: 0.8823 (tttm) REVERT: J 5 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.6016 (ppt170) REVERT: J 8 SER cc_start: 0.9037 (m) cc_final: 0.8779 (t) REVERT: J 10 TYR cc_start: 0.8494 (t80) cc_final: 0.8182 (t80) REVERT: J 11 GLU cc_start: 0.7930 (pt0) cc_final: 0.7647 (mm-30) REVERT: J 28 LYS cc_start: 0.9143 (tttt) cc_final: 0.8223 (tppt) REVERT: K 5 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.6353 (pmt170) REVERT: K 28 LYS cc_start: 0.9047 (tttt) cc_final: 0.8258 (tppt) outliers start: 7 outliers final: 5 residues processed: 110 average time/residue: 2.4086 time to fit residues: 271.2511 Evaluate side-chains 112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2970 Z= 0.238 Angle : 0.478 3.752 3970 Z= 0.275 Chirality : 0.050 0.138 400 Planarity : 0.002 0.019 530 Dihedral : 5.881 19.966 390 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.07 % Allowed : 20.34 % Favored : 77.59 % 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 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.004 0.001 PHE I 4 TYR 0.013 0.001 TYR I 10 ARG 0.002 0.000 ARG G 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: 6 poor density : 110 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.6343 (mmp-170) REVERT: A 28 LYS cc_start: 0.9236 (tttt) cc_final: 0.8965 (tttp) REVERT: B 5 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.6736 (mmp-170) REVERT: C 5 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7926 (mtp85) REVERT: C 8 SER cc_start: 0.8548 (m) cc_final: 0.8029 (t) REVERT: E 8 SER cc_start: 0.8687 (m) cc_final: 0.7688 (t) REVERT: E 11 GLU cc_start: 0.8333 (pt0) cc_final: 0.7741 (pt0) REVERT: E 28 LYS cc_start: 0.9036 (tttt) cc_final: 0.8574 (ttpt) REVERT: F 11 GLU cc_start: 0.8205 (pt0) cc_final: 0.7889 (pt0) REVERT: I 1 ASP cc_start: 0.7970 (p0) cc_final: 0.7671 (p0) REVERT: I 8 SER cc_start: 0.8826 (m) cc_final: 0.7745 (m) REVERT: I 11 GLU cc_start: 0.8086 (pt0) cc_final: 0.7514 (pt0) REVERT: I 28 LYS cc_start: 0.9145 (tttt) cc_final: 0.8821 (tttm) REVERT: J 5 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.6010 (ppt170) REVERT: J 10 TYR cc_start: 0.8467 (t80) cc_final: 0.8135 (t80) REVERT: J 28 LYS cc_start: 0.9136 (tttt) cc_final: 0.8204 (tppt) REVERT: K 5 ARG cc_start: 0.8567 (mtt-85) cc_final: 0.6336 (pmt170) REVERT: K 28 LYS cc_start: 0.9044 (tttt) cc_final: 0.8272 (tppt) outliers start: 6 outliers final: 5 residues processed: 110 average time/residue: 2.3217 time to fit residues: 261.8517 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 : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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 26 SER 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 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2970 Z= 0.264 Angle : 0.480 4.002 3970 Z= 0.277 Chirality : 0.050 0.136 400 Planarity : 0.002 0.014 530 Dihedral : 5.816 18.802 390 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.76 % Allowed : 21.72 % Favored : 75.52 % 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: -2.24 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.004 0.001 PHE D 4 TYR 0.010 0.001 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 115 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.6296 (mmp-170) REVERT: A 11 GLU cc_start: 0.7447 (pt0) cc_final: 0.7229 (pt0) REVERT: A 28 LYS cc_start: 0.9240 (tttt) cc_final: 0.8960 (tttp) REVERT: B 5 ARG cc_start: 0.8341 (mtt-85) cc_final: 0.6509 (mmp-170) REVERT: B 15 GLN cc_start: 0.8600 (pt0) cc_final: 0.8397 (pt0) REVERT: C 5 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7892 (mtp85) REVERT: C 8 SER cc_start: 0.8541 (m) cc_final: 0.8048 (t) REVERT: D 8 SER cc_start: 0.8924 (m) cc_final: 0.8683 (t) REVERT: E 8 SER cc_start: 0.8675 (m) cc_final: 0.8055 (t) REVERT: E 28 LYS cc_start: 0.9044 (tttt) cc_final: 0.8613 (ttpt) REVERT: F 3 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6812 (tm-30) REVERT: F 11 GLU cc_start: 0.8250 (pt0) cc_final: 0.7725 (pt0) REVERT: F 23 ASP cc_start: 0.7819 (m-30) cc_final: 0.7496 (m-30) REVERT: I 1 ASP cc_start: 0.7996 (p0) cc_final: 0.7680 (p0) REVERT: I 28 LYS cc_start: 0.9153 (tttt) cc_final: 0.8829 (tttm) REVERT: J 5 ARG cc_start: 0.8430 (mtt-85) cc_final: 0.6011 (ppt170) REVERT: J 28 LYS cc_start: 0.9194 (tttt) cc_final: 0.8259 (tppt) REVERT: K 5 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.6353 (pmt170) REVERT: K 28 LYS cc_start: 0.9044 (tttt) cc_final: 0.8277 (tppt) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 2.3517 time to fit residues: 260.2549 Evaluate side-chains 114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 26 SER 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 K residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 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 ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2970 Z= 0.280 Angle : 0.484 4.373 3970 Z= 0.279 Chirality : 0.050 0.135 400 Planarity : 0.002 0.014 530 Dihedral : 5.838 20.213 390 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.41 % Allowed : 24.48 % 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: -2.39 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 13 PHE 0.005 0.001 PHE I 4 TYR 0.013 0.001 TYR G 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 115 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.6264 (mmp-170) REVERT: A 28 LYS cc_start: 0.9257 (tttt) cc_final: 0.8979 (tttp) REVERT: B 5 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.6526 (mmp-170) REVERT: C 5 ARG cc_start: 0.8260 (mtt-85) cc_final: 0.7931 (mtp85) REVERT: C 11 GLU cc_start: 0.7997 (pt0) cc_final: 0.7789 (pt0) REVERT: E 8 SER cc_start: 0.8721 (m) cc_final: 0.8132 (t) REVERT: E 28 LYS cc_start: 0.9063 (tttt) cc_final: 0.8638 (ttpt) REVERT: F 3 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6848 (tm-30) REVERT: F 11 GLU cc_start: 0.8170 (pt0) cc_final: 0.7698 (pt0) REVERT: F 23 ASP cc_start: 0.7829 (m-30) cc_final: 0.7500 (m-30) REVERT: I 1 ASP cc_start: 0.8026 (p0) cc_final: 0.7746 (p0) REVERT: I 28 LYS cc_start: 0.9172 (tttt) cc_final: 0.8847 (tttp) REVERT: J 5 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.6018 (ppt170) REVERT: J 28 LYS cc_start: 0.9209 (tttt) cc_final: 0.8268 (tppt) REVERT: K 5 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.6378 (pmt170) REVERT: K 28 LYS cc_start: 0.9056 (tttt) cc_final: 0.8285 (tppt) outliers start: 7 outliers final: 6 residues processed: 109 average time/residue: 2.3374 time to fit residues: 261.0907 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 : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 26 SER 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 K residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4276 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= 0.291 Angle : 0.518 5.312 3970 Z= 0.298 Chirality : 0.050 0.137 400 Planarity : 0.002 0.017 530 Dihedral : 5.846 18.884 390 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.07 % Allowed : 28.28 % 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: -2.45 (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 G 13 PHE 0.009 0.001 PHE I 4 TYR 0.012 0.001 TYR J 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 115 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.6262 (mmp-170) REVERT: A 28 LYS cc_start: 0.9257 (tttt) cc_final: 0.8982 (tttp) REVERT: B 5 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.6440 (mmp-170) REVERT: C 5 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7895 (mtp85) REVERT: C 11 GLU cc_start: 0.7960 (pt0) cc_final: 0.7743 (pt0) REVERT: D 5 ARG cc_start: 0.8625 (ttt90) cc_final: 0.8394 (ttt-90) REVERT: E 8 SER cc_start: 0.8703 (m) cc_final: 0.8123 (t) REVERT: E 28 LYS cc_start: 0.9090 (tttt) cc_final: 0.8655 (ttpt) REVERT: F 4 PHE cc_start: 0.7928 (m-10) cc_final: 0.7370 (m-80) REVERT: F 11 GLU cc_start: 0.8207 (pt0) cc_final: 0.7732 (pt0) REVERT: F 23 ASP cc_start: 0.7810 (m-30) cc_final: 0.7547 (m-30) REVERT: G 23 ASP cc_start: 0.7906 (m-30) cc_final: 0.7342 (m-30) REVERT: I 1 ASP cc_start: 0.8021 (p0) cc_final: 0.7738 (p0) REVERT: I 3 GLU cc_start: 0.7925 (mp0) cc_final: 0.7685 (mp0) REVERT: I 28 LYS cc_start: 0.9171 (tttt) cc_final: 0.8844 (tttm) REVERT: J 5 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.6045 (ppt170) REVERT: J 28 LYS cc_start: 0.9252 (tttt) cc_final: 0.8327 (tppt) REVERT: K 3 GLU cc_start: 0.8008 (mp0) cc_final: 0.7780 (mp0) REVERT: K 5 ARG cc_start: 0.8607 (mtt-85) cc_final: 0.6389 (pmt170) REVERT: K 28 LYS cc_start: 0.9070 (tttt) cc_final: 0.8319 (tppt) outliers start: 6 outliers final: 5 residues processed: 110 average time/residue: 2.3314 time to fit residues: 262.7422 Evaluate side-chains 114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 26 SER 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 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 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 ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2970 Z= 0.366 Angle : 0.544 5.492 3970 Z= 0.315 Chirality : 0.050 0.139 400 Planarity : 0.002 0.016 530 Dihedral : 6.082 19.283 390 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.07 % Allowed : 30.00 % Favored : 67.93 % 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: -2.70 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 13 PHE 0.008 0.001 PHE A 4 TYR 0.013 0.001 TYR K 10 ARG 0.002 0.000 ARG G 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 112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.6484 (mmp-170) REVERT: A 28 LYS cc_start: 0.9258 (tttt) cc_final: 0.8980 (tttp) REVERT: C 5 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7985 (ttt-90) REVERT: C 7 ASP cc_start: 0.8130 (m-30) cc_final: 0.7913 (m-30) REVERT: C 11 GLU cc_start: 0.8024 (pt0) cc_final: 0.7784 (pt0) REVERT: E 8 SER cc_start: 0.8740 (m) cc_final: 0.8198 (t) REVERT: E 28 LYS cc_start: 0.9090 (tttt) cc_final: 0.8635 (ttpt) REVERT: F 11 GLU cc_start: 0.8237 (pt0) cc_final: 0.7708 (pt0) REVERT: F 23 ASP cc_start: 0.7877 (m-30) cc_final: 0.7602 (m-30) REVERT: G 23 ASP cc_start: 0.7909 (m-30) cc_final: 0.7334 (m-30) REVERT: I 1 ASP cc_start: 0.8029 (p0) cc_final: 0.7763 (p0) REVERT: I 28 LYS cc_start: 0.9175 (tttt) cc_final: 0.8844 (tttp) REVERT: J 5 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.6061 (ppt170) REVERT: J 28 LYS cc_start: 0.9250 (tttt) cc_final: 0.8325 (tppt) REVERT: K 5 ARG cc_start: 0.8637 (mtt-85) cc_final: 0.6397 (pmt170) REVERT: K 28 LYS cc_start: 0.9079 (tttt) cc_final: 0.8317 (tppt) outliers start: 6 outliers final: 6 residues processed: 107 average time/residue: 2.3004 time to fit residues: 252.3285 Evaluate side-chains 112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 G 15 GLN ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2970 Z= 0.321 Angle : 0.571 6.505 3970 Z= 0.326 Chirality : 0.050 0.137 400 Planarity : 0.002 0.022 530 Dihedral : 5.979 19.235 390 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.41 % Allowed : 30.34 % Favored : 67.24 % 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: -2.76 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 13 PHE 0.011 0.001 PHE I 4 TYR 0.013 0.002 TYR J 10 ARG 0.002 0.000 ARG B 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 114 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.6489 (mmp-170) REVERT: A 28 LYS cc_start: 0.9258 (tttt) cc_final: 0.8974 (tttp) REVERT: C 5 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.8028 (ttt-90) REVERT: C 7 ASP cc_start: 0.8154 (m-30) cc_final: 0.7940 (m-30) REVERT: C 11 GLU cc_start: 0.8040 (pt0) cc_final: 0.7792 (pt0) REVERT: E 8 SER cc_start: 0.8703 (m) cc_final: 0.7698 (t) REVERT: E 11 GLU cc_start: 0.8215 (pt0) cc_final: 0.7674 (pt0) REVERT: E 28 LYS cc_start: 0.9093 (tttt) cc_final: 0.8664 (ttpt) REVERT: F 4 PHE cc_start: 0.7826 (m-10) cc_final: 0.7395 (m-80) REVERT: F 11 GLU cc_start: 0.8184 (pt0) cc_final: 0.7765 (pt0) REVERT: F 23 ASP cc_start: 0.7816 (m-30) cc_final: 0.7601 (m-30) REVERT: G 23 ASP cc_start: 0.7924 (m-30) cc_final: 0.7365 (m-30) REVERT: I 28 LYS cc_start: 0.9174 (tttt) cc_final: 0.8841 (tttp) REVERT: J 5 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.6088 (ppt170) REVERT: J 28 LYS cc_start: 0.9250 (tttt) cc_final: 0.8321 (tppt) REVERT: K 5 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.6330 (pmt170) REVERT: K 28 LYS cc_start: 0.9072 (tttt) cc_final: 0.8310 (tppt) outliers start: 7 outliers final: 6 residues processed: 108 average time/residue: 2.2580 time to fit residues: 250.2224 Evaluate side-chains 112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.1980 chunk 17 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4571 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= 0.254 Angle : 0.578 6.199 3970 Z= 0.326 Chirality : 0.050 0.137 400 Planarity : 0.002 0.013 530 Dihedral : 5.806 19.823 390 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.07 % Allowed : 31.72 % Favored : 66.21 % 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: -2.69 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 13 PHE 0.007 0.001 PHE I 4 TYR 0.011 0.001 TYR I 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 112 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.6530 (mmp-170) REVERT: A 28 LYS cc_start: 0.9265 (tttt) cc_final: 0.9024 (tttp) REVERT: B 5 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.6659 (mmp-170) REVERT: C 7 ASP cc_start: 0.8073 (m-30) cc_final: 0.7860 (m-30) REVERT: C 11 GLU cc_start: 0.8005 (pt0) cc_final: 0.7746 (pt0) REVERT: C 28 LYS cc_start: 0.9172 (tttp) cc_final: 0.8720 (ttmt) REVERT: E 3 GLU cc_start: 0.8118 (tt0) cc_final: 0.7338 (tm-30) REVERT: E 8 SER cc_start: 0.8637 (m) cc_final: 0.7991 (t) REVERT: E 11 GLU cc_start: 0.8198 (pt0) cc_final: 0.7657 (pt0) REVERT: E 28 LYS cc_start: 0.9107 (tttt) cc_final: 0.8677 (ttpt) REVERT: F 4 PHE cc_start: 0.7722 (m-10) cc_final: 0.7424 (m-80) REVERT: F 11 GLU cc_start: 0.8230 (pt0) cc_final: 0.7969 (pt0) REVERT: F 23 ASP cc_start: 0.7813 (m-30) cc_final: 0.7600 (m-30) REVERT: G 23 ASP cc_start: 0.7892 (m-30) cc_final: 0.7268 (m-30) REVERT: I 28 LYS cc_start: 0.9169 (tttt) cc_final: 0.8837 (tttm) REVERT: J 5 ARG cc_start: 0.8466 (mtt-85) cc_final: 0.6095 (ppt170) REVERT: J 28 LYS cc_start: 0.9243 (tttt) cc_final: 0.8308 (tppt) REVERT: K 5 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.6333 (pmt170) REVERT: K 28 LYS cc_start: 0.9074 (tttt) cc_final: 0.8304 (tppt) outliers start: 6 outliers final: 6 residues processed: 107 average time/residue: 2.3718 time to fit residues: 260.5666 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 : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 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 = 0.3831 r_free = 0.3831 target = 0.098406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089667 restraints weight = 14330.403| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.68 r_work: 0.3591 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2970 Z= 0.331 Angle : 0.573 5.323 3970 Z= 0.327 Chirality : 0.050 0.150 400 Planarity : 0.002 0.020 530 Dihedral : 5.941 20.628 390 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.07 % Allowed : 32.07 % Favored : 65.86 % 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 C 13 PHE 0.011 0.001 PHE I 4 TYR 0.014 0.002 TYR J 10 ARG 0.002 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5537.93 seconds wall clock time: 98 minutes 12.25 seconds (5892.25 seconds total)