Starting phenix.real_space_refine on Wed Jan 17 23:45:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8j_23717/01_2024/7m8j_23717.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8j_23717/01_2024/7m8j_23717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8j_23717/01_2024/7m8j_23717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8j_23717/01_2024/7m8j_23717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8j_23717/01_2024/7m8j_23717.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8j_23717/01_2024/7m8j_23717.pdb" } resolution = 3.48 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= -0.008 sd= 0.083 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 14 5.16 5 C 2238 2.51 5 N 589 2.21 5 O 676 1.98 5 H 3398 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 98": "OD1" <-> "OD2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6915 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3541 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Chain: "H" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1799 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1575 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Time building chain proxies: 3.70, per 1000 atoms: 0.54 Number of scatterers: 6915 At special positions: 0 Unit cell: (100.1, 74.8, 94.6, 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 14 16.00 O 676 8.00 N 589 7.00 C 2238 6.00 H 3398 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 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: 6.96 Conformation dependent library (CDL) restraints added in 732.0 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 3.1% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.232A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.013A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.985A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.247A pdb=" N GLU H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.020A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.020A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.025A pdb=" N VAL L 19 " --> pdb=" O ILE L 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 91 " --> pdb=" O VAL L 19 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 282 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: 2.42 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 3398 1.04 - 1.26: 569 1.26 - 1.47: 1552 1.47 - 1.69: 1466 1.69 - 1.91: 20 Bond restraints: 7005 Sorted by residual: bond pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 1.808 1.906 -0.098 3.30e-02 9.18e+02 8.80e+00 bond pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 1.808 1.718 0.090 3.30e-02 9.18e+02 7.51e+00 bond pdb=" CG GLN H 72 " pdb=" CD GLN H 72 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.97e+00 bond pdb=" CB ASP A 111 " pdb=" CG ASP A 111 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.23e-02 6.61e+03 1.84e+00 ... (remaining 7000 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.48: 153 106.48 - 113.42: 7967 113.42 - 120.37: 2318 120.37 - 127.31: 2101 127.31 - 134.25: 53 Bond angle restraints: 12592 Sorted by residual: angle pdb=" N PHE H 71 " pdb=" CA PHE H 71 " pdb=" C PHE H 71 " ideal model delta sigma weight residual 113.28 119.15 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N CYS A 131 " pdb=" CA CYS A 131 " pdb=" C CYS A 131 " ideal model delta sigma weight residual 109.07 102.45 6.62 1.52e+00 4.33e-01 1.90e+01 angle pdb=" N THR A 167 " pdb=" CA THR A 167 " pdb=" C THR A 167 " ideal model delta sigma weight residual 110.80 118.99 -8.19 2.13e+00 2.20e-01 1.48e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 122.89 -8.49 2.30e+00 1.89e-01 1.36e+01 angle pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 110.39 116.08 -5.69 1.75e+00 3.27e-01 1.06e+01 ... (remaining 12587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3000 17.94 - 35.88: 221 35.88 - 53.81: 41 53.81 - 71.75: 6 71.75 - 89.69: 3 Dihedral angle restraints: 3271 sinusoidal: 1694 harmonic: 1577 Sorted by residual: dihedral pdb=" CA LYS A 97 " pdb=" C LYS A 97 " pdb=" N SER A 98 " pdb=" CA SER A 98 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE H 71 " pdb=" C PHE H 71 " pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PRO A 217 " pdb=" C PRO A 217 " pdb=" N GLN A 218 " pdb=" CA GLN A 218 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 3268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 341 0.044 - 0.088: 131 0.088 - 0.131: 53 0.131 - 0.175: 10 0.175 - 0.219: 3 Chirality restraints: 538 Sorted by residual: chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA CYS A 131 " pdb=" N CYS A 131 " pdb=" C CYS A 131 " pdb=" CB CYS A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS A 113 " pdb=" N LYS A 113 " pdb=" C LYS A 113 " pdb=" CB LYS A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 535 not shown) Planarity restraints: 1053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 95 " 0.033 9.50e-02 1.11e+02 3.47e-02 2.44e+01 pdb=" NE ARG H 95 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG H 95 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 95 " -0.076 2.00e-02 2.50e+03 pdb=" NH2 ARG H 95 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG H 95 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG H 95 " 0.058 2.00e-02 2.50e+03 pdb="HH21 ARG H 95 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG H 95 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 69 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLN H 69 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN H 69 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS H 70 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 75 " 0.005 9.50e-02 1.11e+02 2.28e-02 1.16e+01 pdb=" NE ARG H 75 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 75 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 75 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG H 75 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG H 75 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG H 75 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG H 75 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 75 " 0.044 2.00e-02 2.50e+03 ... (remaining 1050 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 171 2.10 - 2.73: 11573 2.73 - 3.35: 17850 3.35 - 3.98: 22465 3.98 - 4.60: 35263 Nonbonded interactions: 87322 Sorted by model distance: nonbonded pdb=" OD2 ASP A 111 " pdb=" HZ1 LYS A 113 " model vdw 1.481 1.850 nonbonded pdb=" O ARG A 21 " pdb="HE22 GLN A 23 " model vdw 1.488 1.850 nonbonded pdb=" OD2 ASP A 111 " pdb=" HZ3 LYS A 113 " model vdw 1.573 1.850 nonbonded pdb=" O PRO L 15 " pdb="HE22 GLN L 17 " model vdw 1.659 1.850 nonbonded pdb=" OE1 GLN H 72 " pdb=" H GLN H 72 " model vdw 1.701 1.850 ... (remaining 87317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.510 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: 18.800 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 0.098 3607 Z= 0.407 Angle : 0.960 8.488 4906 Z= 0.538 Chirality : 0.055 0.219 538 Planarity : 0.005 0.037 627 Dihedral : 14.719 89.686 1268 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -0.32 (0.37), residues: 443 helix: None (None), residues: 0 sheet: 1.25 (0.38), residues: 172 loop : -1.30 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP L 41 HIS 0.013 0.003 HIS L 115 PHE 0.016 0.003 PHE L 118 TYR 0.021 0.004 TYR H 28 ARG 0.045 0.008 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.734 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2910 time to fit residues: 15.8830 Evaluate side-chains 34 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 185 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3607 Z= 0.189 Angle : 0.654 4.887 4906 Z= 0.357 Chirality : 0.046 0.158 538 Planarity : 0.004 0.024 627 Dihedral : 6.406 22.755 485 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.03 % Allowed : 6.72 % Favored : 92.25 % 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: -0.10 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.18 (0.38), residues: 177 loop : -1.01 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.007 0.002 HIS L 115 PHE 0.013 0.001 PHE A 92 TYR 0.010 0.001 TYR A 145 ARG 0.004 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7985 (t0) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.2759 time to fit residues: 14.4472 Evaluate side-chains 37 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3607 Z= 0.236 Angle : 0.600 5.401 4906 Z= 0.326 Chirality : 0.044 0.145 538 Planarity : 0.003 0.025 627 Dihedral : 5.999 21.161 485 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.03 % Allowed : 8.79 % Favored : 90.18 % 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: -0.25 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 1.05 (0.39), residues: 171 loop : -1.04 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.009 0.001 PHE A 86 TYR 0.011 0.001 TYR A 266 ARG 0.003 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.607 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.2751 time to fit residues: 14.0092 Evaluate side-chains 36 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 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 146 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3607 Z= 0.258 Angle : 0.578 5.399 4906 Z= 0.314 Chirality : 0.044 0.143 538 Planarity : 0.003 0.027 627 Dihedral : 5.656 20.579 485 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.29 % Allowed : 12.14 % Favored : 86.56 % 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: -0.54 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.94 (0.39), residues: 167 loop : -1.28 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.012 0.001 PHE A 86 TYR 0.013 0.002 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.606 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.3014 time to fit residues: 15.0065 Evaluate side-chains 36 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 10 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3607 Z= 0.158 Angle : 0.539 6.294 4906 Z= 0.286 Chirality : 0.043 0.141 538 Planarity : 0.003 0.022 627 Dihedral : 5.251 18.740 485 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.52 % Allowed : 14.47 % Favored : 85.01 % 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: -0.55 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.95 (0.39), residues: 167 loop : -1.30 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.007 0.001 PHE A 92 TYR 0.007 0.001 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.626 Fit side-chains REVERT: A 96 GLU cc_start: 0.8406 (tp30) cc_final: 0.8094 (tp30) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.2974 time to fit residues: 13.9658 Evaluate side-chains 34 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3607 Z= 0.230 Angle : 0.540 5.025 4906 Z= 0.290 Chirality : 0.043 0.144 538 Planarity : 0.003 0.024 627 Dihedral : 5.147 18.420 485 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.29 % Allowed : 14.21 % Favored : 84.50 % 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: -0.55 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.94 (0.38), residues: 172 loop : -1.33 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.011 0.001 PHE A 86 TYR 0.011 0.001 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.664 Fit side-chains REVERT: A 96 GLU cc_start: 0.8539 (tp30) cc_final: 0.8201 (tp30) REVERT: A 187 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7552 (mttp) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.3000 time to fit residues: 15.4460 Evaluate side-chains 37 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3607 Z= 0.200 Angle : 0.534 4.947 4906 Z= 0.286 Chirality : 0.043 0.141 538 Planarity : 0.003 0.022 627 Dihedral : 5.048 18.680 485 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.81 % Allowed : 14.47 % Favored : 83.72 % 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: -0.57 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.98 (0.37), residues: 172 loop : -1.39 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.009 0.001 PHE A 86 TYR 0.009 0.001 TYR A 266 ARG 0.004 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.597 Fit side-chains REVERT: A 96 GLU cc_start: 0.8550 (tp30) cc_final: 0.8243 (tp30) REVERT: A 187 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7456 (mttp) REVERT: H 11 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7096 (pt0) outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 0.2867 time to fit residues: 14.9567 Evaluate side-chains 40 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3607 Z= 0.160 Angle : 0.520 5.802 4906 Z= 0.275 Chirality : 0.043 0.138 538 Planarity : 0.003 0.021 627 Dihedral : 4.892 18.912 485 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.78 % Allowed : 16.02 % Favored : 83.20 % 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: -0.42 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.29 (0.38), residues: 168 loop : -1.41 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.004 0.001 HIS L 115 PHE 0.007 0.001 PHE A 92 TYR 0.007 0.001 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.571 Fit side-chains REVERT: A 96 GLU cc_start: 0.8405 (tp30) cc_final: 0.8135 (tp30) REVERT: H 11 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7041 (pt0) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.2692 time to fit residues: 14.4353 Evaluate side-chains 36 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3607 Z= 0.187 Angle : 0.519 4.854 4906 Z= 0.276 Chirality : 0.043 0.141 538 Planarity : 0.003 0.020 627 Dihedral : 4.854 18.790 485 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.03 % Allowed : 16.28 % Favored : 82.69 % 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: -0.42 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.28 (0.38), residues: 170 loop : -1.42 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.008 0.001 PHE A 86 TYR 0.008 0.001 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.643 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.2660 time to fit residues: 13.7537 Evaluate side-chains 37 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 35 optimal weight: 0.0980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3607 Z= 0.142 Angle : 0.499 4.825 4906 Z= 0.264 Chirality : 0.043 0.137 538 Planarity : 0.003 0.022 627 Dihedral : 4.667 19.675 485 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.29 % Allowed : 16.28 % Favored : 82.43 % 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: -0.27 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 1.45 (0.39), residues: 170 loop : -1.38 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.004 0.001 HIS L 115 PHE 0.007 0.001 PHE A 92 TYR 0.006 0.001 TYR A 91 ARG 0.004 0.000 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.5816 (t0) REVERT: H 11 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7097 (pt0) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.2704 time to fit residues: 13.5648 Evaluate side-chains 37 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.0020 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082285 restraints weight = 21260.001| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.53 r_work: 0.3119 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3607 Z= 0.168 Angle : 0.500 4.772 4906 Z= 0.265 Chirality : 0.042 0.141 538 Planarity : 0.003 0.023 627 Dihedral : 4.645 19.330 485 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.03 % Allowed : 17.05 % Favored : 81.91 % 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: -0.18 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 1.49 (0.39), residues: 170 loop : -1.29 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.004 0.001 HIS L 115 PHE 0.007 0.001 PHE A 86 TYR 0.007 0.001 TYR H 103 ARG 0.004 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2769.38 seconds wall clock time: 50 minutes 10.41 seconds (3010.41 seconds total)