Starting phenix.real_space_refine on Thu Sep 10 23:58:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_22235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_22235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_22235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_22235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_22235.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_22235.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2026/6xl6_22235.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 10 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: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.62, per 1000 atoms: 0.30 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: 0.58 Conformation dependent library (CDL) restraints added in 203.2 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: 0.73 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: 1.02 Time building geometry restraints manager: 0.77 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=" C3' DG T 43 " pdb=" C2' DG T 43 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DT N 61 " pdb=" O3' DT N 61 " ideal model delta sigma weight residual 1.435 1.473 -0.038 1.30e-02 5.92e+03 8.76e+00 bond pdb=" C3' DG N 55 " pdb=" C2' DG N 55 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.70e+00 bond pdb=" C3' DC T 34 " pdb=" C2' DC T 34 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.08e+00 bond pdb=" C3' DC T 29 " pdb=" O3' DC T 29 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.32e+00 ... (remaining 5680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 7405 1.38 - 2.75: 436 2.75 - 4.13: 50 4.13 - 5.50: 8 5.50 - 6.88: 9 Bond angle restraints: 7908 Sorted by residual: angle pdb=" O4' DC T 30 " pdb=" C4' DC T 30 " pdb=" C3' DC T 30 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.80e+01 angle pdb=" O4' DT T 38 " pdb=" C4' DT T 38 " pdb=" C3' DT T 38 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT N 45 " pdb=" C4 DT N 45 " pdb=" O4 DT N 45 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT N 62 " pdb=" C4 DT N 62 " pdb=" O4 DT N 62 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 7903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.07: 2963 32.07 - 64.14: 253 64.14 - 96.21: 14 96.21 - 128.28: 0 128.28 - 160.35: 1 Dihedral angle restraints: 3231 sinusoidal: 1635 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 3228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 577 0.041 - 0.082: 198 0.082 - 0.123: 76 0.123 - 0.164: 19 0.164 - 0.204: 6 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.330 Find NCS groups from input model: 0.080 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:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5685 Z= 0.417 Angle : 0.730 6.880 7908 Z= 0.521 Chirality : 0.051 0.204 876 Planarity : 0.004 0.053 832 Dihedral : 20.332 160.349 2203 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.001 ARG G 80 TYR 0.019 0.001 TYR H 127 PHE 0.011 0.002 PHE H 190 TRP 0.014 0.002 TRP H 229 HIS 0.004 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.42 ( 5685) covalent geometry : angle 0.72956 / 0.52 ( 7908) hydrogen bonds : bond 0.16374 / 18.15 ( 306) hydrogen bonds : angle 6.91504 / 9.41 ( 884) *********************** 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 : 0.168 Fit side-chains REVERT: G 23 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7730 (ptmt) REVERT: G 82 ARG cc_start: 0.8131 (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: 0.7128 time to fit residues: 40.7035 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 : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 53 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3510 r_free = 0.3510 target = 0.112325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095376 restraints weight = 5969.389| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.55 r_work: 0.3134 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5685 Z= 0.157 Angle : 0.560 6.030 7908 Z= 0.336 Chirality : 0.042 0.213 876 Planarity : 0.004 0.048 832 Dihedral : 22.491 163.063 1089 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.82 % Allowed : 13.06 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.34), residues: 532 helix: 0.59 (0.34), residues: 230 sheet: -1.66 (0.47), residues: 94 loop : -0.99 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 56 TYR 0.020 0.001 TYR H 127 PHE 0.008 0.001 PHE H 166 TRP 0.014 0.001 TRP H 229 HIS 0.007 0.001 HIS H 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 ( 5685) covalent geometry : angle 0.56048 / 0.34 ( 7908) hydrogen bonds : bond 0.04895 / 5.34 ( 306) hydrogen bonds : angle 5.07624 / 6.78 ( 884) *********************** 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.200 Fit side-chains REVERT: G 23 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7733 (ptmt) REVERT: G 85 ILE cc_start: 0.9004 (mt) cc_final: 0.8790 (mt) REVERT: G 95 MET cc_start: 0.9130 (mtt) cc_final: 0.8719 (ttm) REVERT: G 112 MET cc_start: 0.7998 (mmm) cc_final: 0.7746 (tpt) REVERT: H 56 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: H 89 ILE cc_start: 0.8754 (mt) cc_final: 0.8433 (mp) REVERT: H 121 ILE cc_start: 0.9006 (mt) cc_final: 0.8696 (mm) REVERT: H 180 ASP cc_start: 0.8094 (t0) cc_final: 0.7846 (t0) REVERT: H 187 VAL cc_start: 0.8798 (t) cc_final: 0.8554 (m) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 0.4480 time to fit residues: 23.6839 Evaluate side-chains 37 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 56 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 104 GLN H 188 ASN H 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095282 restraints weight = 5964.741| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.56 r_work: 0.3130 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5685 Z= 0.162 Angle : 0.536 6.334 7908 Z= 0.320 Chirality : 0.041 0.260 876 Planarity : 0.004 0.045 832 Dihedral : 22.501 161.258 1089 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.63 % Allowed : 13.67 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.36), residues: 532 helix: 1.16 (0.35), residues: 230 sheet: -1.45 (0.49), residues: 94 loop : -0.75 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 220 TYR 0.022 0.001 TYR H 223 PHE 0.009 0.001 PHE H 166 TRP 0.014 0.001 TRP H 229 HIS 0.003 0.001 HIS H 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 ( 5685) covalent geometry : angle 0.53601 / 0.32 ( 7908) hydrogen bonds : bond 0.04249 / 4.60 ( 306) hydrogen bonds : angle 4.74497 / 6.31 ( 884) *********************** 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 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.205 Fit side-chains REVERT: G 23 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7726 (ptmt) REVERT: G 85 ILE cc_start: 0.9010 (mt) cc_final: 0.8799 (mt) REVERT: G 95 MET cc_start: 0.9106 (mtt) cc_final: 0.8693 (ttm) REVERT: H 56 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7543 (mtp180) REVERT: H 89 ILE cc_start: 0.8723 (mt) cc_final: 0.8402 (mp) REVERT: H 187 VAL cc_start: 0.8782 (t) cc_final: 0.8533 (m) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.5529 time to fit residues: 27.3022 Evaluate side-chains 38 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 56 ARG Chi-restraints excluded: chain H residue 240 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095407 restraints weight = 5996.806| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.56 r_work: 0.3132 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5685 Z= 0.157 Angle : 0.530 6.291 7908 Z= 0.314 Chirality : 0.041 0.257 876 Planarity : 0.004 0.044 832 Dihedral : 22.528 161.334 1089 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.45 % Allowed : 13.88 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.36), residues: 532 helix: 1.35 (0.35), residues: 232 sheet: -1.24 (0.53), residues: 86 loop : -0.65 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 81 TYR 0.019 0.001 TYR H 127 PHE 0.009 0.001 PHE H 131 TRP 0.013 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 ( 5685) covalent geometry : angle 0.53024 / 0.31 ( 7908) hydrogen bonds : bond 0.04011 / 4.32 ( 306) hydrogen bonds : angle 4.56715 / 6.07 ( 884) *********************** 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.193 Fit side-chains REVERT: G 12 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8064 (mtm180) REVERT: G 23 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7743 (ptmt) REVERT: G 85 ILE cc_start: 0.9016 (mt) cc_final: 0.8807 (mt) REVERT: G 95 MET cc_start: 0.9126 (mtt) cc_final: 0.8747 (ttm) REVERT: H 56 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7578 (mtp180) REVERT: H 89 ILE cc_start: 0.8737 (mt) cc_final: 0.8392 (mp) REVERT: H 121 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8524 (mm) REVERT: H 187 VAL cc_start: 0.8774 (t) cc_final: 0.8532 (m) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 0.5218 time to fit residues: 25.8586 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 : 0.159 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 240 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095119 restraints weight = 6009.548| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.56 r_work: 0.3129 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5685 Z= 0.162 Angle : 0.531 6.360 7908 Z= 0.312 Chirality : 0.041 0.261 876 Planarity : 0.004 0.043 832 Dihedral : 22.548 160.964 1089 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.65 % Allowed : 15.92 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.36), residues: 532 helix: 1.52 (0.35), residues: 232 sheet: -1.11 (0.53), residues: 90 loop : -0.50 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 130 TYR 0.027 0.001 TYR H 223 PHE 0.008 0.001 PHE H 131 TRP 0.014 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 5685) covalent geometry : angle 0.53121 / 0.31 ( 7908) hydrogen bonds : bond 0.03936 / 4.24 ( 306) hydrogen bonds : angle 4.47713 / 5.95 ( 884) *********************** 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: 13 poor density : 37 time to evaluate : 0.195 Fit side-chains REVERT: G 12 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8055 (mtm180) REVERT: G 23 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7756 (ptmt) REVERT: G 85 ILE cc_start: 0.9022 (mt) cc_final: 0.8820 (mt) REVERT: G 95 MET cc_start: 0.9099 (mtt) cc_final: 0.8730 (ttm) REVERT: H 56 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7580 (mtp180) REVERT: H 89 ILE cc_start: 0.8738 (mt) cc_final: 0.8395 (mp) REVERT: H 121 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8531 (mm) REVERT: H 187 VAL cc_start: 0.8776 (t) cc_final: 0.8549 (m) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.4585 time to fit residues: 22.8923 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 13 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094243 restraints weight = 6020.878| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.56 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5685 Z= 0.184 Angle : 0.547 6.401 7908 Z= 0.317 Chirality : 0.041 0.264 876 Planarity : 0.004 0.044 832 Dihedral : 22.608 160.642 1089 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.47 % Allowed : 15.92 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.36), residues: 532 helix: 1.61 (0.35), residues: 232 sheet: -1.07 (0.54), residues: 90 loop : -0.47 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 242 TYR 0.021 0.001 TYR H 127 PHE 0.009 0.001 PHE H 166 TRP 0.014 0.002 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 5685) covalent geometry : angle 0.54658 / 0.32 ( 7908) hydrogen bonds : bond 0.04006 / 4.33 ( 306) hydrogen bonds : angle 4.47097 / 5.93 ( 884) *********************** 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: 17 poor density : 36 time to evaluate : 0.196 Fit side-chains REVERT: G 12 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8100 (mtm180) REVERT: G 23 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7766 (ptmt) REVERT: G 85 ILE cc_start: 0.9021 (mt) cc_final: 0.8819 (mt) REVERT: G 95 MET cc_start: 0.9107 (mtt) cc_final: 0.8719 (ttm) REVERT: H 56 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7586 (mtp180) REVERT: H 89 ILE cc_start: 0.8729 (mt) cc_final: 0.8379 (mp) REVERT: H 121 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8531 (mm) outliers start: 17 outliers final: 9 residues processed: 49 average time/residue: 0.4518 time to fit residues: 23.5006 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.0170 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 ASN G 51 GLN H 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095676 restraints weight = 6026.523| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.57 r_work: 0.3134 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5685 Z= 0.146 Angle : 0.522 6.702 7908 Z= 0.306 Chirality : 0.040 0.255 876 Planarity : 0.003 0.043 832 Dihedral : 22.562 161.735 1089 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.65 % Allowed : 17.35 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.36), residues: 532 helix: 1.73 (0.35), residues: 232 sheet: -1.02 (0.54), residues: 90 loop : -0.40 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 81 TYR 0.016 0.001 TYR H 127 PHE 0.007 0.001 PHE H 190 TRP 0.013 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 ( 5685) covalent geometry : angle 0.52210 / 0.31 ( 7908) hydrogen bonds : bond 0.03777 / 4.06 ( 306) hydrogen bonds : angle 4.35640 / 5.80 ( 884) *********************** 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: 13 poor density : 38 time to evaluate : 0.159 Fit side-chains REVERT: G 12 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8022 (mtm180) REVERT: G 23 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7758 (ptmt) REVERT: G 85 ILE cc_start: 0.9006 (mt) cc_final: 0.8804 (mt) REVERT: G 95 MET cc_start: 0.9095 (mtt) cc_final: 0.8739 (ttm) REVERT: H 56 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7547 (mtp180) REVERT: H 70 GLN cc_start: 0.7864 (mt0) cc_final: 0.7529 (mt0) REVERT: H 89 ILE cc_start: 0.8751 (mt) cc_final: 0.8425 (mp) REVERT: H 121 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8513 (mm) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.5021 time to fit residues: 24.9023 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain H residue 240 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095763 restraints weight = 6092.706| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.57 r_work: 0.3137 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5685 Z= 0.148 Angle : 0.522 7.475 7908 Z= 0.306 Chirality : 0.040 0.259 876 Planarity : 0.003 0.042 832 Dihedral : 22.478 160.907 1089 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.65 % Allowed : 17.55 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.36), residues: 532 helix: 1.80 (0.35), residues: 232 sheet: -0.96 (0.51), residues: 96 loop : -0.38 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 220 TYR 0.029 0.001 TYR H 223 PHE 0.007 0.001 PHE H 131 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 5685) covalent geometry : angle 0.52186 / 0.31 ( 7908) hydrogen bonds : bond 0.03737 / 4.03 ( 306) hydrogen bonds : angle 4.31092 / 5.74 ( 884) *********************** 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 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.193 Fit side-chains REVERT: G 12 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8029 (mtm180) REVERT: G 23 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7767 (ptmt) REVERT: G 85 ILE cc_start: 0.9010 (mt) cc_final: 0.8807 (mt) REVERT: G 95 MET cc_start: 0.9127 (mtt) cc_final: 0.8773 (ttm) REVERT: H 56 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7545 (mtp180) REVERT: H 70 GLN cc_start: 0.7879 (mt0) cc_final: 0.7538 (mt0) REVERT: H 89 ILE cc_start: 0.8752 (mt) cc_final: 0.8430 (mp) REVERT: H 121 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8504 (mm) outliers start: 13 outliers final: 10 residues processed: 45 average time/residue: 0.5367 time to fit residues: 25.4632 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096155 restraints weight = 6137.747| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.59 r_work: 0.3141 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5685 Z= 0.144 Angle : 0.508 6.480 7908 Z= 0.301 Chirality : 0.040 0.258 876 Planarity : 0.003 0.042 832 Dihedral : 22.409 160.927 1089 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.65 % Allowed : 17.55 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.36), residues: 532 helix: 1.86 (0.35), residues: 232 sheet: -0.94 (0.51), residues: 96 loop : -0.35 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 81 TYR 0.024 0.001 TYR H 223 PHE 0.007 0.001 PHE H 190 TRP 0.013 0.001 TRP H 229 HIS 0.002 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 5685) covalent geometry : angle 0.50836 / 0.30 ( 7908) hydrogen bonds : bond 0.03693 / 3.99 ( 306) hydrogen bonds : angle 4.27158 / 5.69 ( 884) *********************** 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: 13 poor density : 37 time to evaluate : 0.226 Fit side-chains REVERT: G 12 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8021 (mtm180) REVERT: G 23 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7768 (ptmt) REVERT: G 47 MET cc_start: 0.8684 (tpt) cc_final: 0.8445 (tpp) REVERT: G 85 ILE cc_start: 0.9015 (mt) cc_final: 0.8812 (mt) REVERT: G 95 MET cc_start: 0.9126 (mtt) cc_final: 0.8774 (ttm) REVERT: H 56 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7552 (mtp180) REVERT: H 70 GLN cc_start: 0.7880 (mt0) cc_final: 0.7535 (mt0) REVERT: H 89 ILE cc_start: 0.8774 (mt) cc_final: 0.8456 (mp) REVERT: H 121 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8498 (mm) outliers start: 13 outliers final: 10 residues processed: 46 average time/residue: 0.4879 time to fit residues: 23.7748 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095047 restraints weight = 6146.493| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.58 r_work: 0.3126 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5685 Z= 0.178 Angle : 0.537 6.420 7908 Z= 0.314 Chirality : 0.041 0.265 876 Planarity : 0.004 0.042 832 Dihedral : 22.416 160.171 1089 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.65 % Allowed : 17.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.36), residues: 532 helix: 1.78 (0.35), residues: 232 sheet: -0.88 (0.52), residues: 96 loop : -0.40 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 242 TYR 0.026 0.001 TYR H 223 PHE 0.009 0.001 PHE H 190 TRP 0.013 0.002 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 5685) covalent geometry : angle 0.53694 / 0.31 ( 7908) hydrogen bonds : bond 0.03886 / 4.20 ( 306) hydrogen bonds : angle 4.35771 / 5.80 ( 884) ********************** 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 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.204 Fit side-chains REVERT: G 12 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8059 (mtm180) REVERT: G 23 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7774 (ptmt) REVERT: G 95 MET cc_start: 0.9142 (mtt) cc_final: 0.8770 (ttm) REVERT: H 56 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7573 (mtp180) REVERT: H 70 GLN cc_start: 0.7899 (mt0) cc_final: 0.7585 (mt0) REVERT: H 89 ILE cc_start: 0.8792 (mt) cc_final: 0.8470 (mp) REVERT: H 121 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8502 (mm) outliers start: 13 outliers final: 10 residues processed: 43 average time/residue: 0.4979 time to fit residues: 22.6424 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 51 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.114029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096965 restraints weight = 6103.872| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.59 r_work: 0.3157 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5685 Z= 0.131 Angle : 0.520 9.391 7908 Z= 0.303 Chirality : 0.040 0.251 876 Planarity : 0.003 0.042 832 Dihedral : 22.312 161.670 1089 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.45 % Allowed : 17.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.36), residues: 532 helix: 1.91 (0.35), residues: 232 sheet: -0.88 (0.52), residues: 96 loop : -0.30 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 81 TYR 0.021 0.001 TYR H 223 PHE 0.007 0.001 PHE H 131 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 ( 5685) covalent geometry : angle 0.52048 / 0.30 ( 7908) hydrogen bonds : bond 0.03603 / 3.90 ( 306) hydrogen bonds : angle 4.24176 / 5.66 ( 884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.26 seconds wall clock time: 29 minutes 21.84 seconds (1761.84 seconds total)