Starting phenix.real_space_refine on Thu Mar 6 09:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xl6_22235/03_2025/6xl6_22235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xl6_22235/03_2025/6xl6_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/cci-nas-00/data/ceres_data/6xl6_22235/03_2025/6xl6_22235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xl6_22235/03_2025/6xl6_22235.map" model { file = "/net/cci-nas-00/data/ceres_data/6xl6_22235/03_2025/6xl6_22235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xl6_22235/03_2025/6xl6_22235.cif" } 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. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.99, per 1000 atoms: 0.73 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 651.6 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... Secondary structure from input PDB file: 17 helices and 6 sheets defined 45.1% alpha, 28.2% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.599A pdb=" N LEU G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 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) Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 107 removed outlier: 3.703A pdb=" N ILE G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.666A pdb=" N ILE G 140 " --> pdb=" O PHE G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 154 removed outlier: 3.726A pdb=" N ILE G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) 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 233 removed outlier: 3.939A pdb=" N ALA G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 14 through 25 Processing helix chain 'H' and resid 42 through 57 removed outlier: 3.524A pdb=" N GLN H 51 " --> pdb=" O MET H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.686A pdb=" N THR H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 109 removed outlier: 3.693A pdb=" N ARG H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 154 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 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 218 through 233 removed outlier: 4.304A pdb=" N ALA H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 257 Processing sheet with id=AA1, first strand: chain 'G' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'G' and resid 117 through 121 removed outlier: 4.710A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET G 259 " --> pdb=" O ILE G 246 " (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=AA3, first strand: chain 'G' and resid 117 through 121 removed outlier: 4.710A pdb=" N THR G 206 " --> pdb=" O VAL G 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'H' and resid 117 through 121 removed outlier: 4.962A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) 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=AA6, first strand: chain 'H' and resid 117 through 121 removed outlier: 4.962A pdb=" N THR H 206 " --> pdb=" O VAL H 266 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 762 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: 1.66 Time building geometry restraints manager: 1.65 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: 0.00 - 1.38: 7509 1.38 - 2.75: 341 2.75 - 4.13: 41 4.13 - 5.50: 8 5.50 - 6.88: 9 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: 1210 2.79 - 3.31: 4802 3.31 - 3.84: 9741 3.84 - 4.37: 11491 4.37 - 4.90: 18250 Nonbonded interactions: 45494 Sorted by model distance: nonbonded pdb=" OH TYR G 127 " pdb=" OE2 GLU G 185 " model vdw 2.257 3.040 nonbonded pdb=" O VAL G 28 " pdb=" NE2 GLN G 45 " model vdw 2.276 3.120 nonbonded pdb=" OD1 ASP H 135 " pdb=" OG SER H 138 " model vdw 2.311 3.040 nonbonded pdb=" NE2 HIS H 170 " pdb=" OE1 GLU H 182 " model vdw 2.312 3.120 nonbonded pdb=" OG SER H 128 " pdb=" OE2 GLU H 182 " model vdw 2.368 3.040 ... (remaining 45489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 1.240 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.970 Find NCS groups from input model: 0.170 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- 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= 0.313 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 to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.530 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: 1.4743 time to fit residues: 84.3420 Evaluate side-chains 36 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 193 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095341 restraints weight = 5903.289| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.55 r_work: 0.3133 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5685 Z= 0.213 Angle : 0.526 6.090 7908 Z= 0.300 Chirality : 0.040 0.147 876 Planarity : 0.004 0.050 832 Dihedral : 20.924 161.120 1227 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.02 % Allowed : 12.24 % Favored : 86.73 % 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: -0.37 (0.34), residues: 532 helix: 0.69 (0.34), residues: 230 sheet: -1.35 (0.53), residues: 80 loop : -0.68 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 229 HIS 0.005 0.001 HIS H 170 PHE 0.009 0.001 PHE H 166 TYR 0.018 0.001 TYR H 127 ARG 0.003 0.001 ARG G 56 *********************** 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 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.551 Fit side-chains REVERT: G 23 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7749 (ptmt) REVERT: G 48 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8594 (ttmt) REVERT: G 85 ILE cc_start: 0.9015 (mt) cc_final: 0.8808 (mt) REVERT: G 95 MET cc_start: 0.9148 (mtt) cc_final: 0.8736 (ttm) REVERT: G 112 MET cc_start: 0.8010 (mmm) cc_final: 0.7765 (tpt) REVERT: H 56 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7536 (mtp180) REVERT: H 89 ILE cc_start: 0.8731 (mt) cc_final: 0.8423 (mp) REVERT: H 187 VAL cc_start: 0.8808 (t) cc_final: 0.8562 (m) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 1.1602 time to fit residues: 65.0232 Evaluate side-chains 40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 101 HIS H 154 ASN H 188 ASN H 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094003 restraints weight = 5939.157| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.56 r_work: 0.3110 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5685 Z= 0.268 Angle : 0.539 6.562 7908 Z= 0.303 Chirality : 0.040 0.147 876 Planarity : 0.004 0.048 832 Dihedral : 20.912 160.629 1227 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.84 % Allowed : 14.08 % Favored : 84.08 % 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: -0.10 (0.35), residues: 532 helix: 1.14 (0.35), residues: 230 sheet: -1.39 (0.51), residues: 86 loop : -0.72 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 229 HIS 0.003 0.001 HIS H 170 PHE 0.009 0.001 PHE H 190 TYR 0.022 0.002 TYR H 127 ARG 0.002 0.000 ARG H 39 *********************** 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 to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.741 Fit side-chains REVERT: G 23 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7737 (ptmt) REVERT: G 95 MET cc_start: 0.9105 (mtt) cc_final: 0.8724 (mtt) REVERT: G 112 MET cc_start: 0.7934 (mmm) cc_final: 0.7645 (tpt) REVERT: H 56 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7595 (mtp180) REVERT: H 89 ILE cc_start: 0.8735 (mt) cc_final: 0.8392 (mp) REVERT: H 121 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8545 (mm) REVERT: H 187 VAL cc_start: 0.8819 (t) cc_final: 0.8577 (m) outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 1.1631 time to fit residues: 56.6209 Evaluate side-chains 42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 12 ARG Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 121 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.0050 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.0040 chunk 21 optimal weight: 0.5980 overall best weight: 0.3806 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096954 restraints weight = 6155.883| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.60 r_work: 0.3157 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1610 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= 0.169 Angle : 0.489 6.265 7908 Z= 0.280 Chirality : 0.038 0.136 876 Planarity : 0.003 0.046 832 Dihedral : 20.645 161.610 1227 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.65 % Allowed : 15.31 % Favored : 82.04 % 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: 0.39 (0.36), residues: 532 helix: 1.56 (0.35), residues: 230 sheet: -1.12 (0.50), residues: 96 loop : -0.43 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS H 170 PHE 0.008 0.001 PHE H 131 TYR 0.014 0.001 TYR H 127 ARG 0.002 0.000 ARG H 220 *********************** 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.564 Fit side-chains REVERT: G 12 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8010 (mtm180) REVERT: G 23 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7751 (ptmt) REVERT: G 45 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8521 (mp10) REVERT: G 95 MET cc_start: 0.9141 (mtt) cc_final: 0.8765 (ttm) REVERT: H 56 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7517 (mtp180) REVERT: H 89 ILE cc_start: 0.8697 (mt) cc_final: 0.8364 (mp) REVERT: H 121 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8498 (mm) REVERT: H 187 VAL cc_start: 0.8733 (t) cc_final: 0.8475 (m) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 1.6865 time to fit residues: 88.3608 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG 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 12 ARG Chi-restraints excluded: chain H residue 14 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 49 optimal weight: 0.0010 chunk 38 optimal weight: 0.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- 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 H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097518 restraints weight = 5875.439| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.53 r_work: 0.3169 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1760 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= 0.168 Angle : 0.485 6.336 7908 Z= 0.276 Chirality : 0.038 0.136 876 Planarity : 0.003 0.044 832 Dihedral : 20.637 160.868 1227 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.45 % Allowed : 16.33 % Favored : 81.22 % 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: 0.63 (0.36), residues: 532 helix: 1.79 (0.35), residues: 230 sheet: -1.00 (0.50), residues: 96 loop : -0.34 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 PHE 0.009 0.001 PHE H 131 TYR 0.017 0.001 TYR H 223 ARG 0.001 0.000 ARG H 220 *********************** 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.610 Fit side-chains REVERT: G 12 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7999 (mtm180) REVERT: G 23 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7774 (ptmt) REVERT: G 95 MET cc_start: 0.9129 (mtt) cc_final: 0.8765 (ttm) REVERT: H 56 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7510 (mtp180) REVERT: H 89 ILE cc_start: 0.8736 (mt) cc_final: 0.8409 (mp) REVERT: H 121 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8477 (mm) REVERT: H 187 VAL cc_start: 0.8864 (t) cc_final: 0.8664 (m) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 1.0369 time to fit residues: 51.6292 Evaluate side-chains 43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 181 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096268 restraints weight = 5818.976| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.53 r_work: 0.3149 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1750 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= 0.207 Angle : 0.498 6.400 7908 Z= 0.282 Chirality : 0.039 0.137 876 Planarity : 0.003 0.043 832 Dihedral : 20.694 160.643 1227 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.65 % Allowed : 17.14 % Favored : 80.20 % 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: 0.74 (0.36), residues: 532 helix: 1.91 (0.35), residues: 230 sheet: -0.96 (0.51), residues: 96 loop : -0.32 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 PHE 0.008 0.001 PHE H 131 TYR 0.018 0.001 TYR H 127 ARG 0.001 0.000 ARG H 39 *********************** 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.816 Fit side-chains REVERT: G 12 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8012 (mtm180) REVERT: G 23 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7774 (ptmt) REVERT: G 95 MET cc_start: 0.9130 (mtt) cc_final: 0.8785 (ttm) REVERT: H 56 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7520 (mtp180) REVERT: H 70 GLN cc_start: 0.7891 (mt0) cc_final: 0.7542 (mt0) REVERT: H 89 ILE cc_start: 0.8754 (mt) cc_final: 0.8441 (mp) REVERT: H 121 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8479 (mm) outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 1.5798 time to fit residues: 81.1449 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG 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 12 ARG Chi-restraints excluded: chain H residue 14 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095851 restraints weight = 5932.412| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.55 r_work: 0.3140 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1773 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= 0.214 Angle : 0.508 6.381 7908 Z= 0.285 Chirality : 0.039 0.137 876 Planarity : 0.003 0.043 832 Dihedral : 20.733 160.938 1227 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.86 % Allowed : 17.55 % 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: 0.76 (0.36), residues: 532 helix: 1.94 (0.35), residues: 230 sheet: -0.90 (0.51), residues: 96 loop : -0.35 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 229 HIS 0.003 0.001 HIS H 105 PHE 0.008 0.001 PHE H 190 TYR 0.019 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.524 Fit side-chains REVERT: G 12 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8003 (mtm180) REVERT: G 23 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7775 (ptmt) REVERT: G 47 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8589 (tpp) REVERT: G 95 MET cc_start: 0.9130 (mtt) cc_final: 0.8771 (ttm) REVERT: H 56 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7530 (mtp180) REVERT: H 70 GLN cc_start: 0.7934 (mt0) cc_final: 0.7586 (mt0) REVERT: H 89 ILE cc_start: 0.8751 (mt) cc_final: 0.8440 (mp) REVERT: H 121 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8477 (mm) outliers start: 14 outliers final: 10 residues processed: 46 average time/residue: 1.1069 time to fit residues: 53.8447 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG 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 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 56 ARG Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 VAL 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 54 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.095696 restraints weight = 5869.590| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.53 r_work: 0.3139 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1789 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= 0.222 Angle : 0.513 6.577 7908 Z= 0.287 Chirality : 0.039 0.137 876 Planarity : 0.004 0.043 832 Dihedral : 20.754 160.884 1227 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.27 % Allowed : 17.96 % Favored : 78.78 % 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: 0.77 (0.36), residues: 532 helix: 1.94 (0.35), residues: 230 sheet: -0.91 (0.51), residues: 96 loop : -0.34 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 PHE 0.009 0.001 PHE H 190 TYR 0.027 0.001 TYR H 223 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 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.586 Fit side-chains REVERT: G 12 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8044 (mtm180) REVERT: G 23 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7774 (ptmt) REVERT: G 47 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8619 (tpp) REVERT: G 95 MET cc_start: 0.9135 (mtt) cc_final: 0.8780 (ttm) REVERT: H 56 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7532 (mtp180) REVERT: H 70 GLN cc_start: 0.8028 (mt0) cc_final: 0.7687 (mt0) REVERT: H 89 ILE cc_start: 0.8758 (mt) cc_final: 0.8448 (mp) REVERT: H 121 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8478 (mm) outliers start: 16 outliers final: 11 residues processed: 49 average time/residue: 1.1862 time to fit residues: 61.5542 Evaluate side-chains 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG 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 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 56 ARG Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 VAL 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 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN G 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095976 restraints weight = 5942.393| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.55 r_work: 0.3143 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5685 Z= 0.218 Angle : 0.529 10.004 7908 Z= 0.291 Chirality : 0.039 0.137 876 Planarity : 0.004 0.043 832 Dihedral : 20.734 160.952 1227 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.86 % Allowed : 18.78 % 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: 0.83 (0.36), residues: 532 helix: 2.01 (0.35), residues: 230 sheet: -0.89 (0.51), residues: 96 loop : -0.33 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 PHE 0.009 0.001 PHE H 190 TYR 0.024 0.001 TYR H 223 ARG 0.002 0.000 ARG G 81 *********************** 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.667 Fit side-chains REVERT: G 12 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8040 (mtm180) REVERT: G 23 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7781 (ptmt) REVERT: G 47 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8607 (tpp) REVERT: G 95 MET cc_start: 0.9129 (mtt) cc_final: 0.8793 (ttm) REVERT: H 56 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7525 (mtp180) REVERT: H 70 GLN cc_start: 0.7991 (mt0) cc_final: 0.7642 (mt0) REVERT: H 89 ILE cc_start: 0.8751 (mt) cc_final: 0.8437 (mp) REVERT: H 121 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8474 (mm) REVERT: H 151 MET cc_start: 0.7243 (mmm) cc_final: 0.6182 (ptm) outliers start: 14 outliers final: 10 residues processed: 45 average time/residue: 1.9613 time to fit residues: 93.0742 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 181 VAL 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 56 ARG Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 VAL 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 37 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.097140 restraints weight = 5911.442| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.55 r_work: 0.3162 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1954 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= 0.189 Angle : 0.514 10.010 7908 Z= 0.284 Chirality : 0.039 0.137 876 Planarity : 0.003 0.043 832 Dihedral : 20.636 160.681 1227 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.65 % Allowed : 19.39 % Favored : 77.96 % 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: 0.90 (0.36), residues: 532 helix: 2.01 (0.35), residues: 232 sheet: -0.84 (0.51), residues: 96 loop : -0.23 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 PHE 0.009 0.001 PHE H 131 TYR 0.022 0.001 TYR H 223 ARG 0.002 0.000 ARG G 242 ********************** 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 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.591 Fit side-chains REVERT: G 12 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8022 (mtm180) REVERT: G 23 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7784 (ptmt) REVERT: G 47 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8582 (tpp) REVERT: G 95 MET cc_start: 0.9072 (mtt) cc_final: 0.8672 (ttm) REVERT: H 56 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7450 (mmp-170) REVERT: H 70 GLN cc_start: 0.7964 (mt0) cc_final: 0.7611 (mt0) REVERT: H 79 GLU cc_start: 0.7921 (tp30) cc_final: 0.7303 (mt-10) REVERT: H 89 ILE cc_start: 0.8740 (mt) cc_final: 0.8432 (mp) REVERT: H 121 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8451 (mm) REVERT: H 151 MET cc_start: 0.7019 (mmm) cc_final: 0.6283 (ptm) REVERT: H 188 ASN cc_start: 0.7858 (m-40) cc_final: 0.7515 (m110) outliers start: 13 outliers final: 10 residues processed: 50 average time/residue: 1.1739 time to fit residues: 61.7640 Evaluate side-chains 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG 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 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 56 ARG Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 VAL 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 53 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.096455 restraints weight = 5915.019| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.54 r_work: 0.3150 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1960 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= 0.210 Angle : 0.523 9.706 7908 Z= 0.287 Chirality : 0.040 0.145 876 Planarity : 0.003 0.043 832 Dihedral : 20.671 160.650 1227 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.86 % Allowed : 19.39 % Favored : 77.76 % 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: 0.91 (0.36), residues: 532 helix: 2.02 (0.35), residues: 232 sheet: -0.82 (0.51), residues: 96 loop : -0.24 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 PHE 0.009 0.001 PHE H 190 TYR 0.021 0.001 TYR H 223 ARG 0.002 0.000 ARG G 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3922.76 seconds wall clock time: 70 minutes 2.17 seconds (4202.17 seconds total)