Starting phenix.real_space_refine on Sun Mar 10 21:59:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl6_22235/03_2024/6xl6_22235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl6_22235/03_2024/6xl6_22235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl6_22235/03_2024/6xl6_22235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl6_22235/03_2024/6xl6_22235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl6_22235/03_2024/6xl6_22235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl6_22235/03_2024/6xl6_22235_updated.pdb" } resolution = 3.0 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= 0.004 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: 6 Type Number sf(0) Gaussians Sb 2 10.97 5 P 44 5.49 5 S 26 5.16 5 C 3386 2.51 5 N 912 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ASP 94": "OD1" <-> "OD2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 135": "OD1" <-> "OD2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 231": "OE1" <-> "OE2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H ARG 220": "NH1" <-> "NH2" Residue "H TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H GLU 267": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5456 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2208 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 255} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'118': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.69, per 1000 atoms: 0.68 Number of scatterers: 5456 At special positions: 0 Unit cell: (110.639, 103.974, 69.316, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sb 2 50.95 S 26 16.00 P 44 15.00 O 1086 8.00 N 912 7.00 C 3386 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: 2.36 Conformation dependent library (CDL) restraints added in 915.5 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 4 sheets defined 40.9% alpha, 19.6% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'G' and resid 4 through 11 Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.540A pdb=" N LYS G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN G 51 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 106 Processing helix chain 'G' and resid 136 through 153 removed outlier: 3.666A pdb=" N ILE G 140 " --> pdb=" O PHE G 136 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE G 143 " --> pdb=" O TYR G 139 " (cutoff:3.500A) Proline residue: G 144 - end of helix removed outlier: 3.604A pdb=" N MET G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 232 Processing helix chain 'H' and resid 4 through 10 Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 43 through 58 removed outlier: 3.524A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.686A pdb=" N THR H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 108 removed outlier: 3.693A pdb=" N ARG H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 153 Proline residue: H 144 - end of helix removed outlier: 3.545A pdb=" N VAL H 150 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 232 removed outlier: 5.143A pdb=" N ARG H 220 " --> pdb=" O ASP H 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN H 221 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 232 " --> pdb=" O TRP H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'G' and resid 117 through 121 removed outlier: 6.705A pdb=" N GLU G 261 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR G 245 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN G 263 " --> pdb=" O GLU G 243 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU G 243 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N CYS G 165 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET G 179 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL G 181 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE G 125 " --> pdb=" O VAL G 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 235 through 237 Processing sheet with id= C, first strand: chain 'H' and resid 117 through 121 removed outlier: 5.105A pdb=" N CYS H 165 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE H 125 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 235 through 237 218 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 2332 1.40 - 1.58: 3215 1.58 - 1.77: 88 1.77 - 1.95: 42 1.95 - 2.13: 8 Bond restraints: 5685 Sorted by residual: bond pdb="SB 118 H 302 " pdb=" C1C 118 H 302 " ideal model delta sigma weight residual 2.092 2.133 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb="SB 118 G 302 " pdb=" C1C 118 G 302 " ideal model delta sigma weight residual 2.092 2.131 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb="SB 118 G 302 " pdb=" C1D 118 G 302 " ideal model delta sigma weight residual 2.092 2.129 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb="SB 118 H 302 " pdb=" C1D 118 H 302 " ideal model delta sigma weight residual 2.092 2.126 -0.034 2.00e-02 2.50e+03 2.86e+00 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 416 106.40 - 113.30: 3068 113.30 - 120.21: 2127 120.21 - 127.11: 2155 127.11 - 134.01: 142 Bond angle restraints: 7908 Sorted by residual: angle pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sigma weight residual 120.20 124.47 -4.27 1.50e+00 4.44e-01 8.12e+00 angle pdb=" N PRO H 144 " pdb=" CA PRO H 144 " pdb=" C PRO H 144 " ideal model delta sigma weight residual 110.70 114.05 -3.35 1.22e+00 6.72e-01 7.54e+00 angle pdb=" C ILE H 143 " pdb=" CA ILE H 143 " pdb=" CB ILE H 143 " ideal model delta sigma weight residual 114.00 110.47 3.53 1.31e+00 5.83e-01 7.27e+00 angle pdb=" C LEU G 27 " pdb=" N VAL G 28 " pdb=" CA VAL G 28 " ideal model delta sigma weight residual 123.04 120.70 2.34 9.20e-01 1.18e+00 6.50e+00 angle pdb=" CA TYR H 127 " pdb=" CB TYR H 127 " pdb=" CG TYR H 127 " ideal model delta sigma weight residual 113.90 118.43 -4.53 1.80e+00 3.09e-01 6.32e+00 ... (remaining 7903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 3095 32.07 - 64.14: 259 64.14 - 96.21: 14 96.21 - 128.28: 0 128.28 - 160.35: 1 Dihedral angle restraints: 3369 sinusoidal: 1773 harmonic: 1596 Sorted by residual: dihedral pdb=" CA VAL G 126 " pdb=" C VAL G 126 " pdb=" N TYR G 127 " pdb=" CA TYR G 127 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DT N 61 " pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " pdb=" P DT N 62 " ideal model delta sinusoidal sigma weight residual 220.00 59.65 160.35 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA ILE H 205 " pdb=" C ILE H 205 " pdb=" N THR H 206 " pdb=" CA THR H 206 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 3366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 617 0.041 - 0.082: 188 0.082 - 0.123: 51 0.123 - 0.164: 15 0.164 - 0.204: 5 Chirality restraints: 876 Sorted by residual: chirality pdb=" C13 1N7 H 301 " pdb=" C12 1N7 H 301 " pdb=" C14 1N7 H 301 " pdb=" O2 1N7 H 301 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C6 1N7 H 301 " pdb=" C18 1N7 H 301 " pdb=" C5 1N7 H 301 " pdb=" C7 1N7 H 301 " both_signs ideal model delta sigma weight residual False -2.43 -2.63 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" C13 1N7 G 301 " pdb=" C12 1N7 G 301 " pdb=" C14 1N7 G 301 " pdb=" O2 1N7 G 301 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 873 not shown) Planarity restraints: 832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO G 144 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO G 145 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 145 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR G 161 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C THR G 161 " 0.028 2.00e-02 2.50e+03 pdb=" O THR G 161 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO G 162 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 28 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO H 29 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 29 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 29 " -0.020 5.00e-02 4.00e+02 ... (remaining 829 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1214 2.79 - 3.31: 4835 3.31 - 3.84: 9767 3.84 - 4.37: 11529 4.37 - 4.90: 18257 Nonbonded interactions: 45602 Sorted by model distance: nonbonded pdb=" OH TYR G 127 " pdb=" OE2 GLU G 185 " model vdw 2.257 2.440 nonbonded pdb=" O VAL G 28 " pdb=" NE2 GLN G 45 " model vdw 2.276 2.520 nonbonded pdb=" OD1 ASP H 135 " pdb=" OG SER H 138 " model vdw 2.311 2.440 nonbonded pdb=" NE2 HIS H 170 " pdb=" OE1 GLU H 182 " model vdw 2.312 2.520 nonbonded pdb=" OG SER H 128 " pdb=" OE2 GLU H 182 " model vdw 2.368 2.440 ... (remaining 45597 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 'G' selection = (chain 'H' and (resid 2 through 269 or (resid 301 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r name O2 or name O3 or name O4 )) or resid 302)) } ncs_group { reference = (chain 'N' and (resid 41 through 50 or resid 52 through 61)) selection = (chain 'T' and (resid 28 through 37 or resid 39 through 48)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.850 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 20.360 Find NCS groups from input model: 0.260 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:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5685 Z= 0.322 Angle : 0.676 6.880 7908 Z= 0.385 Chirality : 0.046 0.204 876 Planarity : 0.004 0.053 832 Dihedral : 19.902 160.349 2341 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.31), residues: 532 helix: -0.79 (0.30), residues: 230 sheet: -1.89 (0.49), residues: 88 loop : -1.34 (0.34), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 229 HIS 0.004 0.001 HIS G 101 PHE 0.011 0.002 PHE H 190 TYR 0.019 0.001 TYR H 127 ARG 0.002 0.001 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.513 Fit side-chains REVERT: G 23 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7730 (ptmt) REVERT: G 82 ARG cc_start: 0.8130 (tmm-80) cc_final: 0.7878 (ttt-90) REVERT: G 85 ILE cc_start: 0.9058 (mt) cc_final: 0.8858 (mt) REVERT: G 95 MET cc_start: 0.9061 (mtt) cc_final: 0.8628 (ttm) REVERT: G 259 MET cc_start: 0.8008 (ttm) cc_final: 0.7801 (ttp) REVERT: H 121 ILE cc_start: 0.8950 (mt) cc_final: 0.8729 (mm) REVERT: H 187 VAL cc_start: 0.8428 (t) cc_final: 0.8227 (m) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 1.4193 time to fit residues: 81.1837 Evaluate side-chains 36 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN G 45 GLN G 51 GLN G 105 HIS G 188 ASN G 233 ASN H 3 GLN H 70 GLN H 86 GLN H 193 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5685 Z= 0.173 Angle : 0.495 6.069 7908 Z= 0.286 Chirality : 0.038 0.141 876 Planarity : 0.004 0.048 832 Dihedral : 20.726 161.726 1227 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.41 % Allowed : 13.06 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.40 (0.34), residues: 532 helix: 0.42 (0.34), residues: 234 sheet: -1.15 (0.54), residues: 84 loop : -0.48 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 229 HIS 0.003 0.001 HIS G 101 PHE 0.008 0.001 PHE H 166 TYR 0.014 0.001 TYR H 127 ARG 0.004 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.520 Fit side-chains REVERT: G 95 MET cc_start: 0.9045 (mtt) cc_final: 0.8662 (ttm) REVERT: H 89 ILE cc_start: 0.8868 (mt) cc_final: 0.8594 (mp) REVERT: H 121 ILE cc_start: 0.8874 (mt) cc_final: 0.8654 (mm) outliers start: 2 outliers final: 3 residues processed: 46 average time/residue: 0.9198 time to fit residues: 45.1671 Evaluate side-chains 37 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.0060 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.0010 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 154 ASN H 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.188 Angle : 0.493 6.740 7908 Z= 0.280 Chirality : 0.038 0.138 876 Planarity : 0.004 0.045 832 Dihedral : 20.581 160.653 1227 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 2.04 % Allowed : 13.67 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.35), residues: 532 helix: 0.60 (0.34), residues: 234 sheet: -1.03 (0.47), residues: 104 loop : -0.43 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 229 HIS 0.003 0.001 HIS G 101 PHE 0.007 0.001 PHE H 166 TYR 0.019 0.001 TYR H 127 ARG 0.002 0.000 ARG G 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.513 Fit side-chains REVERT: G 95 MET cc_start: 0.9014 (mtt) cc_final: 0.8577 (ttm) REVERT: H 89 ILE cc_start: 0.8856 (mt) cc_final: 0.8553 (mp) outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 1.0502 time to fit residues: 52.4086 Evaluate side-chains 39 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5685 Z= 0.218 Angle : 0.495 6.277 7908 Z= 0.281 Chirality : 0.038 0.142 876 Planarity : 0.004 0.043 832 Dihedral : 20.639 160.773 1227 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.06 % Allowed : 13.47 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.35 (0.35), residues: 532 helix: 0.73 (0.34), residues: 234 sheet: -1.07 (0.45), residues: 116 loop : -0.72 (0.39), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 229 HIS 0.002 0.001 HIS G 101 PHE 0.008 0.001 PHE H 166 TYR 0.020 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.573 Fit side-chains REVERT: G 47 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8346 (tpt) REVERT: G 95 MET cc_start: 0.9047 (mtt) cc_final: 0.8613 (ttm) REVERT: H 89 ILE cc_start: 0.8920 (mt) cc_final: 0.8632 (mp) REVERT: H 121 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8411 (mm) outliers start: 15 outliers final: 10 residues processed: 47 average time/residue: 0.8625 time to fit residues: 43.4349 Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5685 Z= 0.223 Angle : 0.496 6.307 7908 Z= 0.280 Chirality : 0.038 0.136 876 Planarity : 0.004 0.041 832 Dihedral : 20.666 160.866 1227 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.27 % Allowed : 15.10 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.35), residues: 532 helix: 0.86 (0.35), residues: 234 sheet: -1.00 (0.46), residues: 116 loop : -0.61 (0.40), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 229 HIS 0.002 0.001 HIS G 101 PHE 0.009 0.001 PHE H 190 TYR 0.020 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.519 Fit side-chains REVERT: G 47 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8103 (tpt) REVERT: G 95 MET cc_start: 0.9057 (mtt) cc_final: 0.8693 (ttm) REVERT: H 89 ILE cc_start: 0.8910 (mt) cc_final: 0.8616 (mp) REVERT: H 121 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8456 (mm) outliers start: 16 outliers final: 10 residues processed: 49 average time/residue: 0.8057 time to fit residues: 42.5399 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 240 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN G 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.197 Angle : 0.490 6.344 7908 Z= 0.277 Chirality : 0.038 0.138 876 Planarity : 0.004 0.040 832 Dihedral : 20.589 160.950 1227 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.88 % Allowed : 15.31 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.04 (0.35), residues: 532 helix: 0.95 (0.35), residues: 234 sheet: -0.88 (0.46), residues: 116 loop : -0.53 (0.40), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 229 HIS 0.002 0.001 HIS G 101 PHE 0.007 0.001 PHE H 166 TYR 0.017 0.001 TYR H 127 ARG 0.001 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 0.612 Fit side-chains REVERT: G 47 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8130 (tpt) REVERT: G 95 MET cc_start: 0.9036 (mtt) cc_final: 0.8674 (ttm) REVERT: H 56 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7369 (mtp180) REVERT: H 89 ILE cc_start: 0.8917 (mt) cc_final: 0.8631 (mp) REVERT: H 121 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8443 (mm) outliers start: 19 outliers final: 11 residues processed: 51 average time/residue: 0.9119 time to fit residues: 49.6966 Evaluate side-chains 51 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 260 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5685 Z= 0.244 Angle : 0.510 6.344 7908 Z= 0.286 Chirality : 0.039 0.136 876 Planarity : 0.004 0.040 832 Dihedral : 20.694 160.692 1227 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.67 % Allowed : 16.94 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.02 (0.35), residues: 532 helix: 0.96 (0.35), residues: 234 sheet: -0.83 (0.47), residues: 116 loop : -0.54 (0.40), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 PHE 0.011 0.001 PHE H 190 TYR 0.021 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 36 time to evaluate : 0.600 Fit side-chains REVERT: G 47 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8167 (tpt) REVERT: G 95 MET cc_start: 0.9017 (mtt) cc_final: 0.8646 (ttm) REVERT: H 89 ILE cc_start: 0.8922 (mt) cc_final: 0.8637 (mp) REVERT: H 121 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8458 (mm) outliers start: 18 outliers final: 12 residues processed: 47 average time/residue: 0.8376 time to fit residues: 42.3612 Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 35 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 260 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.202 Angle : 0.496 6.523 7908 Z= 0.279 Chirality : 0.038 0.137 876 Planarity : 0.004 0.039 832 Dihedral : 20.612 161.014 1227 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.27 % Allowed : 17.14 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.07 (0.35), residues: 532 helix: 1.01 (0.35), residues: 234 sheet: -0.76 (0.47), residues: 116 loop : -0.48 (0.40), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 229 HIS 0.003 0.001 HIS G 101 PHE 0.007 0.001 PHE H 166 TYR 0.018 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.588 Fit side-chains REVERT: G 95 MET cc_start: 0.9032 (mtt) cc_final: 0.8605 (ttm) REVERT: H 89 ILE cc_start: 0.8909 (mt) cc_final: 0.8628 (mp) REVERT: H 121 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8442 (mm) outliers start: 16 outliers final: 12 residues processed: 47 average time/residue: 0.8125 time to fit residues: 41.1442 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 260 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5685 Z= 0.176 Angle : 0.482 6.683 7908 Z= 0.273 Chirality : 0.038 0.135 876 Planarity : 0.004 0.039 832 Dihedral : 20.499 160.841 1227 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.06 % Allowed : 17.76 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.36), residues: 532 helix: 1.08 (0.35), residues: 234 sheet: -0.69 (0.48), residues: 116 loop : -0.41 (0.41), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 229 HIS 0.003 0.001 HIS G 101 PHE 0.010 0.001 PHE H 190 TYR 0.016 0.001 TYR H 127 ARG 0.002 0.000 ARG G 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.503 Fit side-chains REVERT: G 95 MET cc_start: 0.9032 (mtt) cc_final: 0.8623 (ttm) REVERT: H 56 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7484 (mtp180) REVERT: H 70 GLN cc_start: 0.7813 (mt0) cc_final: 0.7513 (mt0) REVERT: H 89 ILE cc_start: 0.8896 (mt) cc_final: 0.8615 (mp) REVERT: H 121 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8421 (mm) outliers start: 15 outliers final: 11 residues processed: 49 average time/residue: 0.9175 time to fit residues: 47.7569 Evaluate side-chains 48 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 0.0010 chunk 18 optimal weight: 2.9990 overall best weight: 0.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5685 Z= 0.156 Angle : 0.482 6.828 7908 Z= 0.273 Chirality : 0.038 0.134 876 Planarity : 0.004 0.039 832 Dihedral : 20.327 160.673 1227 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.24 % Allowed : 19.39 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.59 (0.36), residues: 532 helix: 1.19 (0.35), residues: 234 sheet: -0.49 (0.53), residues: 96 loop : 0.08 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 229 HIS 0.003 0.001 HIS G 101 PHE 0.006 0.001 PHE H 131 TYR 0.014 0.001 TYR H 127 ARG 0.005 0.000 ARG G 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.608 Fit side-chains REVERT: G 95 MET cc_start: 0.9024 (mtt) cc_final: 0.8637 (ttm) REVERT: H 56 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7478 (mtp180) REVERT: H 70 GLN cc_start: 0.7796 (mt0) cc_final: 0.7500 (mt0) REVERT: H 89 ILE cc_start: 0.8876 (mt) cc_final: 0.8600 (mp) outliers start: 11 outliers final: 10 residues processed: 47 average time/residue: 0.9762 time to fit residues: 48.7703 Evaluate side-chains 46 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 260 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095122 restraints weight = 5926.036| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.54 r_work: 0.3126 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5685 Z= 0.253 Angle : 0.524 6.962 7908 Z= 0.292 Chirality : 0.039 0.137 876 Planarity : 0.004 0.040 832 Dihedral : 20.649 160.015 1227 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.04 % Allowed : 19.59 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.26 (0.36), residues: 532 helix: 1.18 (0.35), residues: 234 sheet: -0.69 (0.48), residues: 116 loop : -0.39 (0.41), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 PHE 0.012 0.001 PHE H 190 TYR 0.021 0.001 TYR H 127 ARG 0.003 0.000 ARG G 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.80 seconds wall clock time: 33 minutes 43.51 seconds (2023.51 seconds total)