Starting phenix.real_space_refine on Tue Feb 13 11:04:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys8_10893/02_2024/6ys8_10893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys8_10893/02_2024/6ys8_10893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys8_10893/02_2024/6ys8_10893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys8_10893/02_2024/6ys8_10893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys8_10893/02_2024/6ys8_10893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys8_10893/02_2024/6ys8_10893.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3661 2.51 5 N 882 2.21 5 O 1052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5624 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1695 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 3, 'TRANS': 214} Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1704 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 445 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "F" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 445 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "E" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 445 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 445 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 445 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Time building chain proxies: 3.51, per 1000 atoms: 0.62 Number of scatterers: 5624 At special positions: 0 Unit cell: (70.692, 63.294, 115.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1052 8.00 N 882 7.00 C 3661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.35 Conformation dependent library (CDL) restraints added in 1.0 seconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 72.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 Processing helix chain 'A' and resid 32 through 68 removed outlier: 4.067A pdb=" N SER A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 101 Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.933A pdb=" N PHE A 128 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 196 through 224 Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.906A pdb=" N MET B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 68 removed outlier: 3.954A pdb=" N LEU B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 101 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 134 through 155 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 196 through 225 Processing helix chain 'G' and resid 5 through 28 Processing helix chain 'G' and resid 38 through 56 Processing helix chain 'F' and resid 6 through 30 removed outlier: 4.020A pdb=" N ALA F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 56 removed outlier: 3.633A pdb=" N ILE F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 30 removed outlier: 4.358A pdb=" N ALA E 17 " --> pdb=" O TYR E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 56 Processing helix chain 'D' and resid 5 through 28 Processing helix chain 'D' and resid 38 through 56 Processing helix chain 'C' and resid 8 through 30 Processing helix chain 'C' and resid 41 through 56 removed outlier: 3.776A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 129 423 hydrogen bonds defined for protein. 1260 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: 1.46 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1465 1.34 - 1.45: 998 1.45 - 1.57: 3199 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 5720 Sorted by residual: bond pdb=" N VAL B 32 " pdb=" CA VAL B 32 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N GLY C 38 " pdb=" CA GLY C 38 " ideal model delta sigma weight residual 1.446 1.478 -0.031 1.08e-02 8.57e+03 8.42e+00 bond pdb=" N ILE C 33 " pdb=" CA ILE C 33 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.69e+00 bond pdb=" N ILE A 13 " pdb=" CA ILE A 13 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.14e-02 7.69e+03 7.41e+00 bond pdb=" N ILE B 33 " pdb=" CA ILE B 33 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.79e+00 ... (remaining 5715 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.87: 76 104.87 - 112.57: 2988 112.57 - 120.27: 2389 120.27 - 127.96: 2220 127.96 - 135.66: 27 Bond angle restraints: 7700 Sorted by residual: angle pdb=" C ILE C 33 " pdb=" CA ILE C 33 " pdb=" CB ILE C 33 " ideal model delta sigma weight residual 111.29 135.66 -24.37 1.64e+00 3.72e-01 2.21e+02 angle pdb=" N VAL C 40 " pdb=" CA VAL C 40 " pdb=" C VAL C 40 " ideal model delta sigma weight residual 111.62 105.82 5.80 7.90e-01 1.60e+00 5.40e+01 angle pdb=" C LYS B 30 " pdb=" CA LYS B 30 " pdb=" CB LYS B 30 " ideal model delta sigma weight residual 116.54 110.28 6.26 1.15e+00 7.56e-01 2.96e+01 angle pdb=" C GLU A 31 " pdb=" N VAL A 32 " pdb=" CA VAL A 32 " ideal model delta sigma weight residual 121.97 130.50 -8.53 1.80e+00 3.09e-01 2.25e+01 angle pdb=" N VAL A 32 " pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 109.34 119.12 -9.78 2.08e+00 2.31e-01 2.21e+01 ... (remaining 7695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3008 17.71 - 35.43: 323 35.43 - 53.14: 73 53.14 - 70.86: 13 70.86 - 88.57: 6 Dihedral angle restraints: 3423 sinusoidal: 1310 harmonic: 2113 Sorted by residual: dihedral pdb=" C ILE C 33 " pdb=" N ILE C 33 " pdb=" CA ILE C 33 " pdb=" CB ILE C 33 " ideal model delta harmonic sigma weight residual -122.00 -166.17 44.17 0 2.50e+00 1.60e-01 3.12e+02 dihedral pdb=" N ILE C 33 " pdb=" C ILE C 33 " pdb=" CA ILE C 33 " pdb=" CB ILE C 33 " ideal model delta harmonic sigma weight residual 123.40 161.38 -37.98 0 2.50e+00 1.60e-01 2.31e+02 dihedral pdb=" CD ARG A 9 " pdb=" NE ARG A 9 " pdb=" CZ ARG A 9 " pdb=" NH1 ARG A 9 " ideal model delta sinusoidal sigma weight residual 0.00 88.57 -88.57 1 1.00e+01 1.00e-02 9.36e+01 ... (remaining 3420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 898 0.340 - 0.680: 0 0.680 - 1.020: 0 1.020 - 1.359: 0 1.359 - 1.699: 1 Chirality restraints: 899 Sorted by residual: chirality pdb=" CA ILE C 33 " pdb=" N ILE C 33 " pdb=" C ILE C 33 " pdb=" CB ILE C 33 " both_signs ideal model delta sigma weight residual False 2.43 0.73 1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" CB VAL F 8 " pdb=" CA VAL F 8 " pdb=" CG1 VAL F 8 " pdb=" CG2 VAL F 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL B 32 " pdb=" CA VAL B 32 " pdb=" CG1 VAL B 32 " pdb=" CG2 VAL B 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 896 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 9 " -1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 9 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 9 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 9 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 9 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 9 " -0.526 9.50e-02 1.11e+02 2.36e-01 3.40e+01 pdb=" NE ARG B 9 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 9 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 9 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 9 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 51 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C VAL B 51 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL B 51 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 52 " 0.013 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 8 2.20 - 2.87: 2117 2.87 - 3.55: 8427 3.55 - 4.22: 12386 4.22 - 4.90: 21774 Nonbonded interactions: 44712 Sorted by model distance: nonbonded pdb=" NH2 ARG B 9 " pdb=" OE2 GLU C 49 " model vdw 1.522 2.520 nonbonded pdb=" OE1 GLN A 10 " pdb=" NE2 GLN B 10 " model vdw 1.691 2.520 nonbonded pdb=" CE MET A 12 " pdb=" OE1 GLU E 49 " model vdw 1.804 3.460 nonbonded pdb=" CZ ARG B 9 " pdb=" OE2 GLU C 49 " model vdw 1.880 3.270 nonbonded pdb=" NH1 ARG B 9 " pdb=" OE2 GLU C 49 " model vdw 1.925 2.520 ... (remaining 44707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 7 through 224) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.670 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.006 0.046 5720 Z= 0.393 Angle : 1.035 24.371 7700 Z= 0.619 Chirality : 0.080 1.699 899 Planarity : 0.019 0.492 952 Dihedral : 15.755 88.569 2065 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 2.21 % Allowed : 6.36 % Favored : 91.42 % Rotamer: Outliers : 1.70 % Allowed : 8.67 % Favored : 89.63 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.81 (0.23), residues: 723 helix: -1.92 (0.17), residues: 510 sheet: None (None), residues: 0 loop : -3.73 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 127 HIS 0.004 0.001 HIS B 80 PHE 0.021 0.002 PHE A 20 TYR 0.017 0.002 TYR A 92 ARG 0.001 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 74 LYS cc_start: 0.8950 (tptt) cc_final: 0.8590 (tmmt) REVERT: A 83 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7914 (tp40) REVERT: A 145 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8298 (mm-30) REVERT: A 146 LYS cc_start: 0.8648 (tttm) cc_final: 0.8371 (ttpt) REVERT: A 180 LYS cc_start: 0.8471 (pttt) cc_final: 0.8198 (mtmt) REVERT: A 219 TYR cc_start: 0.8834 (m-10) cc_final: 0.8604 (m-80) REVERT: A 220 ASN cc_start: 0.8721 (m110) cc_final: 0.8509 (m110) REVERT: B 27 ASN cc_start: 0.9271 (t0) cc_final: 0.9060 (t0) REVERT: B 99 GLN cc_start: 0.8702 (tt0) cc_final: 0.8034 (tp40) REVERT: B 123 ASN cc_start: 0.8828 (p0) cc_final: 0.8203 (p0) REVERT: G 7 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8238 (tmtt) REVERT: F 9 MET cc_start: 0.8878 (tpp) cc_final: 0.8349 (tpp) REVERT: F 32 GLU cc_start: 0.8649 (pm20) cc_final: 0.8319 (pm20) REVERT: E 55 LEU cc_start: 0.8974 (pp) cc_final: 0.8710 (mt) REVERT: D 7 LYS cc_start: 0.9280 (mttt) cc_final: 0.8320 (tmtt) REVERT: C 22 VAL cc_start: 0.9571 (p) cc_final: 0.9286 (p) outliers start: 10 outliers final: 6 residues processed: 248 average time/residue: 0.1637 time to fit residues: 52.6268 Evaluate side-chains 217 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.0270 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 220 ASN B 10 GLN B 54 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5720 Z= 0.194 Angle : 0.669 9.056 7700 Z= 0.351 Chirality : 0.041 0.177 899 Planarity : 0.004 0.032 952 Dihedral : 6.339 54.134 776 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 1.24 % Allowed : 4.56 % Favored : 94.19 % Rotamer: Outliers : 3.23 % Allowed : 17.01 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.30), residues: 723 helix: 0.13 (0.21), residues: 523 sheet: None (None), residues: 0 loop : -3.08 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 127 HIS 0.001 0.001 HIS C 30 PHE 0.025 0.002 PHE D 31 TYR 0.015 0.002 TYR B 147 ARG 0.003 0.001 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7350 (ttp) cc_final: 0.5770 (tpp) REVERT: A 74 LYS cc_start: 0.8913 (tptt) cc_final: 0.8569 (tmmt) REVERT: A 83 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7856 (tp40) REVERT: A 145 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8409 (mm-30) REVERT: A 146 LYS cc_start: 0.8625 (tttm) cc_final: 0.8303 (ttpt) REVERT: A 220 ASN cc_start: 0.8701 (m-40) cc_final: 0.8448 (m110) REVERT: B 26 MET cc_start: 0.7797 (mtp) cc_final: 0.7369 (mtm) REVERT: B 99 GLN cc_start: 0.8713 (tt0) cc_final: 0.7572 (tm-30) REVERT: B 123 ASN cc_start: 0.8739 (p0) cc_final: 0.7433 (p0) REVERT: B 124 ILE cc_start: 0.8366 (pt) cc_final: 0.8080 (pt) REVERT: F 4 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7997 (pp) REVERT: F 9 MET cc_start: 0.8920 (tpp) cc_final: 0.8616 (tpp) REVERT: E 9 MET cc_start: 0.8533 (ppp) cc_final: 0.8324 (ppp) REVERT: D 4 LEU cc_start: 0.7170 (mm) cc_final: 0.6895 (mt) REVERT: D 7 LYS cc_start: 0.9372 (mttt) cc_final: 0.8478 (tmtt) REVERT: D 9 MET cc_start: 0.8145 (tpp) cc_final: 0.7811 (mmp) REVERT: D 32 GLU cc_start: 0.8339 (pm20) cc_final: 0.7863 (mp0) REVERT: C 15 MET cc_start: 0.8619 (mmm) cc_final: 0.8163 (tpp) REVERT: C 31 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7728 (m-80) outliers start: 19 outliers final: 11 residues processed: 237 average time/residue: 0.1468 time to fit residues: 46.1257 Evaluate side-chains 217 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 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 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5720 Z= 0.204 Angle : 0.674 8.364 7700 Z= 0.347 Chirality : 0.041 0.176 899 Planarity : 0.003 0.026 952 Dihedral : 5.667 54.760 765 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 1.24 % Allowed : 4.98 % Favored : 93.78 % Rotamer: Outliers : 5.44 % Allowed : 18.88 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.19 (0.31), residues: 723 helix: 0.86 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -2.88 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 127 HIS 0.002 0.001 HIS E 30 PHE 0.021 0.001 PHE D 26 TYR 0.019 0.002 TYR B 147 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7310 (ttp) cc_final: 0.5688 (tpp) REVERT: A 29 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6915 (p) REVERT: A 74 LYS cc_start: 0.8898 (tptt) cc_final: 0.8567 (tmmt) REVERT: A 81 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8854 (mptt) REVERT: A 92 TYR cc_start: 0.8962 (t80) cc_final: 0.8554 (t80) REVERT: A 145 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8454 (mm-30) REVERT: A 146 LYS cc_start: 0.8581 (tttm) cc_final: 0.8300 (mtmt) REVERT: A 217 ASP cc_start: 0.9104 (p0) cc_final: 0.8886 (p0) REVERT: A 220 ASN cc_start: 0.8769 (m-40) cc_final: 0.8503 (m110) REVERT: B 26 MET cc_start: 0.7765 (mtp) cc_final: 0.7357 (mtm) REVERT: B 123 ASN cc_start: 0.8726 (p0) cc_final: 0.8454 (p0) REVERT: G 7 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8513 (ttpt) REVERT: F 4 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8093 (pp) REVERT: F 9 MET cc_start: 0.8902 (tpp) cc_final: 0.8636 (tpp) REVERT: E 9 MET cc_start: 0.8559 (ppp) cc_final: 0.8354 (ppp) REVERT: D 4 LEU cc_start: 0.7178 (mm) cc_final: 0.6911 (mt) REVERT: D 7 LYS cc_start: 0.9363 (mttt) cc_final: 0.8459 (tmtt) REVERT: D 9 MET cc_start: 0.8176 (tpp) cc_final: 0.7824 (mmp) REVERT: D 32 GLU cc_start: 0.8412 (pm20) cc_final: 0.8162 (mp0) REVERT: C 15 MET cc_start: 0.8685 (mmm) cc_final: 0.8206 (tpp) outliers start: 32 outliers final: 20 residues processed: 234 average time/residue: 0.1472 time to fit residues: 45.6987 Evaluate side-chains 225 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5720 Z= 0.191 Angle : 0.674 10.536 7700 Z= 0.340 Chirality : 0.041 0.222 899 Planarity : 0.003 0.025 952 Dihedral : 5.188 58.006 763 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 1.11 % Allowed : 5.12 % Favored : 93.78 % Rotamer: Outliers : 4.59 % Allowed : 25.00 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.30 (0.32), residues: 723 helix: 1.20 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -2.60 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 127 HIS 0.002 0.001 HIS G 30 PHE 0.023 0.001 PHE G 31 TYR 0.030 0.002 TYR A 219 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8890 (tptt) cc_final: 0.8568 (tmmt) REVERT: A 77 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 81 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8785 (mptt) REVERT: A 92 TYR cc_start: 0.8949 (t80) cc_final: 0.8551 (t80) REVERT: A 145 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8565 (mm-30) REVERT: A 146 LYS cc_start: 0.8564 (tttm) cc_final: 0.8338 (mtpt) REVERT: A 217 ASP cc_start: 0.9086 (p0) cc_final: 0.8825 (p0) REVERT: A 220 ASN cc_start: 0.8758 (m-40) cc_final: 0.8473 (m110) REVERT: B 26 MET cc_start: 0.7737 (mtp) cc_final: 0.7350 (mtm) REVERT: B 92 TYR cc_start: 0.8663 (t80) cc_final: 0.8127 (t80) REVERT: G 7 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8587 (tttt) REVERT: G 49 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8456 (mm-30) REVERT: F 4 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8106 (pp) REVERT: F 9 MET cc_start: 0.8958 (tpp) cc_final: 0.8683 (tpp) REVERT: E 9 MET cc_start: 0.8589 (ppp) cc_final: 0.8381 (ppp) REVERT: E 53 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8366 (m-10) REVERT: D 7 LYS cc_start: 0.9357 (mttt) cc_final: 0.8471 (tmtt) REVERT: D 9 MET cc_start: 0.8194 (tpp) cc_final: 0.7955 (mmp) REVERT: C 15 MET cc_start: 0.8643 (mmm) cc_final: 0.8203 (mmm) outliers start: 27 outliers final: 18 residues processed: 230 average time/residue: 0.1426 time to fit residues: 43.9385 Evaluate side-chains 228 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 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 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5720 Z= 0.192 Angle : 0.678 9.553 7700 Z= 0.344 Chirality : 0.041 0.217 899 Planarity : 0.003 0.025 952 Dihedral : 5.081 59.954 763 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 1.11 % Allowed : 4.56 % Favored : 94.33 % Rotamer: Outliers : 5.44 % Allowed : 25.17 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.59 (0.32), residues: 723 helix: 1.39 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -2.46 (0.47), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 127 HIS 0.002 0.001 HIS E 30 PHE 0.020 0.001 PHE C 11 TYR 0.025 0.002 TYR B 147 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7238 (ttp) cc_final: 0.5493 (tpp) REVERT: A 74 LYS cc_start: 0.8872 (tptt) cc_final: 0.8585 (tmmt) REVERT: A 77 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 81 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8868 (mptt) REVERT: A 91 ASP cc_start: 0.7985 (m-30) cc_final: 0.7747 (m-30) REVERT: A 92 TYR cc_start: 0.8938 (t80) cc_final: 0.8600 (t80) REVERT: A 145 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8636 (mm-30) REVERT: A 217 ASP cc_start: 0.9071 (p0) cc_final: 0.8798 (p0) REVERT: A 220 ASN cc_start: 0.8760 (m-40) cc_final: 0.8466 (m110) REVERT: B 26 MET cc_start: 0.7723 (mtp) cc_final: 0.7343 (mtm) REVERT: B 99 GLN cc_start: 0.8793 (tt0) cc_final: 0.8043 (tm-30) REVERT: B 119 ASP cc_start: 0.8571 (t0) cc_final: 0.8352 (t0) REVERT: G 7 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8573 (tttt) REVERT: G 49 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8500 (mm-30) REVERT: F 4 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8172 (pp) REVERT: F 9 MET cc_start: 0.8944 (tpp) cc_final: 0.8651 (tpp) REVERT: E 9 MET cc_start: 0.8602 (ppp) cc_final: 0.8328 (ppp) REVERT: E 41 MET cc_start: 0.8733 (mtp) cc_final: 0.8457 (mtm) REVERT: E 53 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8317 (m-10) REVERT: D 7 LYS cc_start: 0.9356 (mttt) cc_final: 0.8501 (tmtt) REVERT: D 9 MET cc_start: 0.8196 (tpp) cc_final: 0.7856 (mmp) REVERT: C 15 MET cc_start: 0.8612 (mmm) cc_final: 0.8180 (tpp) outliers start: 32 outliers final: 21 residues processed: 236 average time/residue: 0.1496 time to fit residues: 47.0305 Evaluate side-chains 225 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 67 optimal weight: 5.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5720 Z= 0.190 Angle : 0.697 9.925 7700 Z= 0.349 Chirality : 0.042 0.221 899 Planarity : 0.003 0.024 952 Dihedral : 4.963 58.948 763 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 1.11 % Allowed : 4.56 % Favored : 94.33 % Rotamer: Outliers : 4.93 % Allowed : 27.04 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.66 (0.32), residues: 723 helix: 1.47 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -2.50 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 207 HIS 0.002 0.001 HIS E 30 PHE 0.018 0.001 PHE G 31 TYR 0.020 0.002 TYR B 147 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.8507 (tpp) cc_final: 0.8280 (tpp) REVERT: A 26 MET cc_start: 0.7183 (ttp) cc_final: 0.5372 (tpp) REVERT: A 30 LYS cc_start: 0.8718 (mttt) cc_final: 0.7941 (tmtt) REVERT: A 74 LYS cc_start: 0.8865 (tptt) cc_final: 0.8584 (tmmt) REVERT: A 77 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 81 LYS cc_start: 0.9162 (mtpt) cc_final: 0.8873 (mptt) REVERT: A 91 ASP cc_start: 0.7941 (m-30) cc_final: 0.7690 (m-30) REVERT: A 92 TYR cc_start: 0.8916 (t80) cc_final: 0.8600 (t80) REVERT: A 145 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8652 (mm-30) REVERT: A 217 ASP cc_start: 0.9076 (p0) cc_final: 0.8780 (p0) REVERT: A 220 ASN cc_start: 0.8757 (m-40) cc_final: 0.8466 (m110) REVERT: B 26 MET cc_start: 0.7650 (mtp) cc_final: 0.7243 (mtm) REVERT: B 88 GLU cc_start: 0.7862 (tp30) cc_final: 0.7614 (tp30) REVERT: B 99 GLN cc_start: 0.8731 (tt0) cc_final: 0.7975 (tm-30) REVERT: B 119 ASP cc_start: 0.8614 (t0) cc_final: 0.8339 (t0) REVERT: G 7 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8506 (ttpt) REVERT: G 49 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8480 (mm-30) REVERT: F 4 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8198 (pp) REVERT: F 9 MET cc_start: 0.8971 (tpp) cc_final: 0.8693 (tpp) REVERT: E 9 MET cc_start: 0.8589 (ppp) cc_final: 0.8356 (ppp) REVERT: E 49 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8392 (mm-30) REVERT: E 53 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8252 (m-10) REVERT: D 7 LYS cc_start: 0.9353 (mttt) cc_final: 0.8502 (tmtt) REVERT: D 9 MET cc_start: 0.8273 (tpp) cc_final: 0.7848 (mmp) REVERT: C 15 MET cc_start: 0.8605 (mmm) cc_final: 0.8159 (mmm) outliers start: 29 outliers final: 19 residues processed: 225 average time/residue: 0.1450 time to fit residues: 43.8473 Evaluate side-chains 226 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain C residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5720 Z= 0.196 Angle : 0.721 11.385 7700 Z= 0.359 Chirality : 0.043 0.218 899 Planarity : 0.003 0.024 952 Dihedral : 4.821 57.583 761 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 1.11 % Allowed : 4.98 % Favored : 93.91 % Rotamer: Outliers : 4.25 % Allowed : 26.53 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.70 (0.32), residues: 723 helix: 1.42 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -2.38 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.002 0.001 HIS E 30 PHE 0.018 0.001 PHE G 31 TYR 0.021 0.002 TYR B 147 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7085 (ttp) cc_final: 0.5268 (tpp) REVERT: A 30 LYS cc_start: 0.8669 (mttt) cc_final: 0.7878 (tmtt) REVERT: A 74 LYS cc_start: 0.8856 (tptt) cc_final: 0.8586 (tmmt) REVERT: A 77 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 81 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8878 (mptt) REVERT: A 91 ASP cc_start: 0.7913 (m-30) cc_final: 0.7661 (m-30) REVERT: A 92 TYR cc_start: 0.8900 (t80) cc_final: 0.8586 (t80) REVERT: A 145 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8536 (mm-30) REVERT: A 217 ASP cc_start: 0.9081 (p0) cc_final: 0.8758 (p0) REVERT: A 220 ASN cc_start: 0.8774 (m110) cc_final: 0.8410 (m110) REVERT: B 26 MET cc_start: 0.7682 (mtp) cc_final: 0.7324 (mtm) REVERT: B 31 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6440 (pt0) REVERT: B 99 GLN cc_start: 0.8784 (tt0) cc_final: 0.8009 (tm-30) REVERT: B 119 ASP cc_start: 0.8659 (t0) cc_final: 0.8398 (t0) REVERT: G 7 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8493 (ttpt) REVERT: G 49 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8453 (mm-30) REVERT: F 4 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8253 (pp) REVERT: F 9 MET cc_start: 0.8960 (tpp) cc_final: 0.8656 (tpp) REVERT: E 9 MET cc_start: 0.8608 (ppp) cc_final: 0.8373 (ppp) REVERT: E 31 PHE cc_start: 0.5316 (m-10) cc_final: 0.5103 (m-10) REVERT: E 41 MET cc_start: 0.8644 (mtp) cc_final: 0.8441 (mtm) REVERT: E 53 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: D 7 LYS cc_start: 0.9346 (mttt) cc_final: 0.8498 (tmtt) REVERT: D 9 MET cc_start: 0.8249 (tpp) cc_final: 0.7797 (mmp) REVERT: C 15 MET cc_start: 0.8578 (mmm) cc_final: 0.8141 (mmm) outliers start: 25 outliers final: 21 residues processed: 213 average time/residue: 0.1437 time to fit residues: 41.0046 Evaluate side-chains 225 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 31 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 0.0170 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5720 Z= 0.195 Angle : 0.730 11.854 7700 Z= 0.360 Chirality : 0.043 0.218 899 Planarity : 0.003 0.024 952 Dihedral : 4.785 57.011 761 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 1.11 % Allowed : 4.70 % Favored : 94.19 % Rotamer: Outliers : 5.10 % Allowed : 26.70 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.81 (0.32), residues: 723 helix: 1.48 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -2.26 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 127 HIS 0.002 0.001 HIS G 30 PHE 0.021 0.001 PHE C 11 TYR 0.017 0.001 TYR B 147 ARG 0.000 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8582 (mttt) cc_final: 0.7802 (tmtt) REVERT: A 74 LYS cc_start: 0.8862 (tptt) cc_final: 0.8595 (tmmt) REVERT: A 77 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 81 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8868 (mptt) REVERT: A 91 ASP cc_start: 0.7892 (m-30) cc_final: 0.7641 (m-30) REVERT: A 92 TYR cc_start: 0.8863 (t80) cc_final: 0.8594 (t80) REVERT: A 145 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8540 (mm-30) REVERT: A 217 ASP cc_start: 0.9080 (p0) cc_final: 0.8728 (p0) REVERT: A 220 ASN cc_start: 0.8763 (m110) cc_final: 0.8391 (m110) REVERT: B 26 MET cc_start: 0.7668 (mtp) cc_final: 0.6428 (mtm) REVERT: B 31 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6413 (pt0) REVERT: B 99 GLN cc_start: 0.8788 (tt0) cc_final: 0.8010 (tm-30) REVERT: B 119 ASP cc_start: 0.8739 (t0) cc_final: 0.8485 (t0) REVERT: G 7 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8486 (ttpt) REVERT: G 49 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8462 (mm-30) REVERT: F 4 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8274 (pp) REVERT: F 9 MET cc_start: 0.8954 (tpp) cc_final: 0.8651 (tpp) REVERT: E 6 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8651 (mmmt) REVERT: E 9 MET cc_start: 0.8611 (ppp) cc_final: 0.8353 (ppp) REVERT: E 41 MET cc_start: 0.8629 (mtp) cc_final: 0.8311 (mtm) REVERT: E 53 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: D 7 LYS cc_start: 0.9344 (mttt) cc_final: 0.8490 (tmtt) REVERT: D 9 MET cc_start: 0.8234 (tpp) cc_final: 0.7791 (mmp) REVERT: C 15 MET cc_start: 0.8515 (mmm) cc_final: 0.8085 (mmm) outliers start: 30 outliers final: 22 residues processed: 225 average time/residue: 0.1429 time to fit residues: 42.9834 Evaluate side-chains 227 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 31 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5720 Z= 0.200 Angle : 0.740 10.367 7700 Z= 0.363 Chirality : 0.043 0.219 899 Planarity : 0.003 0.041 952 Dihedral : 4.708 56.268 761 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 1.11 % Allowed : 4.70 % Favored : 94.19 % Rotamer: Outliers : 4.76 % Allowed : 28.23 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.90 (0.32), residues: 723 helix: 1.59 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -2.26 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 127 HIS 0.002 0.001 HIS G 30 PHE 0.017 0.001 PHE G 31 TYR 0.016 0.001 TYR D 13 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8584 (mttt) cc_final: 0.7807 (tmtt) REVERT: A 74 LYS cc_start: 0.8859 (tptt) cc_final: 0.8597 (tmmt) REVERT: A 77 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 81 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8873 (mptt) REVERT: A 91 ASP cc_start: 0.7896 (m-30) cc_final: 0.7645 (m-30) REVERT: A 92 TYR cc_start: 0.8810 (t80) cc_final: 0.8521 (t80) REVERT: A 145 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8525 (mm-30) REVERT: A 217 ASP cc_start: 0.9082 (p0) cc_final: 0.8722 (p0) REVERT: A 220 ASN cc_start: 0.8759 (m110) cc_final: 0.8380 (m110) REVERT: B 26 MET cc_start: 0.7348 (mtp) cc_final: 0.6972 (mtm) REVERT: B 99 GLN cc_start: 0.8779 (tt0) cc_final: 0.8024 (tm-30) REVERT: B 119 ASP cc_start: 0.8759 (t0) cc_final: 0.8409 (t0) REVERT: G 7 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8489 (tttt) REVERT: G 49 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8457 (mm-30) REVERT: F 4 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8256 (pp) REVERT: F 9 MET cc_start: 0.8951 (tpp) cc_final: 0.8653 (tpp) REVERT: E 6 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8660 (mmmt) REVERT: E 9 MET cc_start: 0.8617 (ppp) cc_final: 0.8357 (ppp) REVERT: E 53 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: D 7 LYS cc_start: 0.9343 (mttt) cc_final: 0.8490 (tmtt) REVERT: D 9 MET cc_start: 0.8231 (tpp) cc_final: 0.7788 (mmp) REVERT: C 15 MET cc_start: 0.8526 (mmm) cc_final: 0.7974 (mmm) outliers start: 28 outliers final: 23 residues processed: 216 average time/residue: 0.1454 time to fit residues: 41.9459 Evaluate side-chains 223 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 31 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.0040 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5720 Z= 0.240 Angle : 0.773 13.538 7700 Z= 0.377 Chirality : 0.044 0.228 899 Planarity : 0.003 0.034 952 Dihedral : 4.747 56.390 761 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 1.11 % Allowed : 4.98 % Favored : 93.91 % Rotamer: Outliers : 4.76 % Allowed : 27.89 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.84 (0.32), residues: 723 helix: 1.54 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -2.24 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.002 0.001 HIS G 30 PHE 0.017 0.001 PHE G 31 TYR 0.017 0.001 TYR B 147 ARG 0.004 0.001 ARG B 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.8341 (tpp) cc_final: 0.8060 (tpp) REVERT: A 30 LYS cc_start: 0.8607 (mttt) cc_final: 0.7855 (tmtt) REVERT: A 74 LYS cc_start: 0.8893 (tptt) cc_final: 0.8607 (tmmt) REVERT: A 77 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 91 ASP cc_start: 0.8015 (m-30) cc_final: 0.7766 (m-30) REVERT: A 92 TYR cc_start: 0.8903 (t80) cc_final: 0.8556 (t80) REVERT: A 145 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8558 (mm-30) REVERT: A 217 ASP cc_start: 0.9110 (p0) cc_final: 0.8762 (p0) REVERT: A 220 ASN cc_start: 0.8798 (m110) cc_final: 0.8442 (m110) REVERT: B 16 MET cc_start: 0.8807 (mmm) cc_final: 0.8552 (mmm) REVERT: B 26 MET cc_start: 0.7418 (mtp) cc_final: 0.7052 (mtm) REVERT: B 99 GLN cc_start: 0.8795 (tt0) cc_final: 0.8034 (tm-30) REVERT: B 120 ARG cc_start: 0.5980 (mmm-85) cc_final: 0.5657 (mmm160) REVERT: G 7 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8412 (ttpt) REVERT: F 4 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8283 (pp) REVERT: F 9 MET cc_start: 0.8966 (tpp) cc_final: 0.8650 (tpp) REVERT: E 6 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8664 (mmmt) REVERT: E 9 MET cc_start: 0.8614 (ppp) cc_final: 0.8356 (ppp) REVERT: E 53 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: D 7 LYS cc_start: 0.9352 (mttt) cc_final: 0.8502 (tmtt) REVERT: D 9 MET cc_start: 0.8267 (tpp) cc_final: 0.7728 (mmp) REVERT: C 15 MET cc_start: 0.8553 (mmm) cc_final: 0.7983 (mmm) outliers start: 28 outliers final: 25 residues processed: 210 average time/residue: 0.1454 time to fit residues: 40.9568 Evaluate side-chains 223 residues out of total 588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 31 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090711 restraints weight = 12615.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093514 restraints weight = 8367.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093998 restraints weight = 6429.160| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5720 Z= 0.214 Angle : 0.794 12.997 7700 Z= 0.388 Chirality : 0.045 0.218 899 Planarity : 0.003 0.029 952 Dihedral : 4.715 55.129 761 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 1.11 % Allowed : 4.84 % Favored : 94.05 % Rotamer: Outliers : 4.59 % Allowed : 29.25 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.85 (0.32), residues: 723 helix: 1.52 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.21 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 127 HIS 0.002 0.001 HIS G 30 PHE 0.024 0.001 PHE C 11 TYR 0.018 0.001 TYR D 13 ARG 0.005 0.001 ARG B 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1506.69 seconds wall clock time: 27 minutes 58.57 seconds (1678.57 seconds total)