Starting phenix.real_space_refine on Wed Sep 17 06:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xl6_22235/09_2025/6xl6_22235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xl6_22235/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2025/6xl6_22235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2025/6xl6_22235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2025/6xl6_22235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xl6_22235/09_2025/6xl6_22235.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 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: 1.29, per 1000 atoms: 0.24 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: 0.39 Conformation dependent library (CDL) restraints added in 118.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.59 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: 0.69 Time building geometry restraints manager: 0.50 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: 1.090 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- 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= 0.241 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00527 ( 5685) covalent geometry : angle 0.67640 ( 7908) hydrogen bonds : bond 0.16374 ( 306) hydrogen bonds : angle 6.91504 ( 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 : 0.149 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: 0.7519 time to fit residues: 42.7057 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 : 0.193 ------------------------------------------------------------------------------- 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: 0.9990 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... 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 = 0.3516 r_free = 0.3516 target = 0.112869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095999 restraints weight = 5950.740| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.55 r_work: 0.3144 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1123 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= 0.149 Angle : 0.520 6.027 7908 Z= 0.297 Chirality : 0.039 0.147 876 Planarity : 0.004 0.050 832 Dihedral : 20.860 161.268 1227 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.82 % Allowed : 12.24 % Favored : 86.94 % 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 aren not related in a simple way. whole: -0.32 (0.34), residues: 532 helix: 0.72 (0.34), residues: 230 sheet: -1.33 (0.53), residues: 80 loop : -0.65 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 220 TYR 0.015 0.001 TYR H 127 PHE 0.008 0.001 PHE H 166 TRP 0.013 0.001 TRP H 229 HIS 0.005 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5685) covalent geometry : angle 0.52043 ( 7908) hydrogen bonds : bond 0.04064 ( 306) hydrogen bonds : angle 4.83046 ( 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.180 Fit side-chains REVERT: G 23 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7725 (ptmt) REVERT: G 48 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8584 (ttmt) REVERT: G 85 ILE cc_start: 0.9009 (mt) cc_final: 0.8798 (mt) REVERT: G 95 MET cc_start: 0.9142 (mtt) cc_final: 0.8748 (ttm) REVERT: G 112 MET cc_start: 0.8003 (mmm) cc_final: 0.7758 (tpt) REVERT: H 56 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: H 89 ILE cc_start: 0.8721 (mt) cc_final: 0.8412 (mp) REVERT: H 121 ILE cc_start: 0.8985 (mt) cc_final: 0.8688 (mm) REVERT: H 187 VAL cc_start: 0.8782 (t) cc_final: 0.8536 (m) outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.4646 time to fit residues: 25.9229 Evaluate side-chains 39 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 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 = 0.112426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095559 restraints weight = 5914.643| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.54 r_work: 0.3138 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: 0.8125 moved from start: 0.1353 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= 0.162 Angle : 0.512 6.600 7908 Z= 0.290 Chirality : 0.039 0.138 876 Planarity : 0.004 0.047 832 Dihedral : 20.740 160.740 1227 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.43 % Allowed : 13.88 % 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 aren not related in a simple way. whole: -0.00 (0.35), residues: 532 helix: 1.25 (0.35), residues: 230 sheet: -1.22 (0.50), residues: 84 loop : -0.77 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 56 TYR 0.019 0.001 TYR H 127 PHE 0.007 0.001 PHE H 131 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5685) covalent geometry : angle 0.51155 ( 7908) hydrogen bonds : bond 0.03771 ( 306) hydrogen bonds : angle 4.52560 ( 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: 7 poor density : 42 time to evaluate : 0.175 Fit side-chains REVERT: G 12 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8034 (mtm180) REVERT: G 23 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7736 (ptmt) REVERT: G 85 ILE cc_start: 0.9015 (mt) cc_final: 0.8807 (mt) REVERT: G 95 MET cc_start: 0.9128 (mtt) cc_final: 0.8716 (ttm) REVERT: H 56 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7552 (mtp180) REVERT: H 89 ILE cc_start: 0.8723 (mt) cc_final: 0.8384 (mp) REVERT: H 187 VAL cc_start: 0.8781 (t) cc_final: 0.8538 (m) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.6097 time to fit residues: 29.9756 Evaluate side-chains 41 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 56 ARG 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: 0.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN H 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095366 restraints weight = 5955.703| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.55 r_work: 0.3134 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1480 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= 0.170 Angle : 0.517 6.846 7908 Z= 0.290 Chirality : 0.039 0.141 876 Planarity : 0.004 0.047 832 Dihedral : 20.753 160.940 1227 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.65 % Allowed : 14.08 % Favored : 83.27 % 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 aren not related in a simple way. whole: 0.22 (0.35), residues: 532 helix: 1.46 (0.35), residues: 230 sheet: -1.15 (0.50), residues: 84 loop : -0.67 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 81 TYR 0.022 0.001 TYR H 223 PHE 0.009 0.001 PHE H 131 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5685) covalent geometry : angle 0.51741 ( 7908) hydrogen bonds : bond 0.03642 ( 306) hydrogen bonds : angle 4.39807 ( 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 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.216 Fit side-chains REVERT: G 12 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8023 (mtm180) REVERT: G 23 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7750 (ptmt) REVERT: G 95 MET cc_start: 0.9115 (mtt) cc_final: 0.8771 (mtt) REVERT: H 56 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: H 89 ILE cc_start: 0.8702 (mt) cc_final: 0.8370 (mp) REVERT: H 121 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8433 (mm) REVERT: H 187 VAL cc_start: 0.8769 (t) cc_final: 0.8537 (m) outliers start: 13 outliers final: 6 residues processed: 47 average time/residue: 0.5271 time to fit residues: 26.0860 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 : 0.205 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 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 G 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095898 restraints weight = 6099.382| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.58 r_work: 0.3137 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1574 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= 0.161 Angle : 0.502 6.365 7908 Z= 0.283 Chirality : 0.039 0.138 876 Planarity : 0.004 0.045 832 Dihedral : 20.722 160.968 1227 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.45 % Allowed : 15.71 % Favored : 81.84 % 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 aren not related in a simple way. whole: 0.49 (0.36), residues: 532 helix: 1.67 (0.35), residues: 230 sheet: -1.04 (0.50), residues: 96 loop : -0.42 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 81 TYR 0.018 0.001 TYR H 127 PHE 0.008 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 covalent geometry : bond 0.00358 ( 5685) covalent geometry : angle 0.50196 ( 7908) hydrogen bonds : bond 0.03545 ( 306) hydrogen bonds : angle 4.30986 ( 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 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.212 Fit side-chains REVERT: G 12 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8037 (mtm180) REVERT: G 23 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7770 (ptmt) REVERT: G 95 MET cc_start: 0.9100 (mtt) cc_final: 0.8729 (ttm) REVERT: G 173 GLU cc_start: 0.7733 (mp0) cc_final: 0.7437 (pm20) REVERT: H 56 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: H 70 GLN cc_start: 0.7911 (mt0) cc_final: 0.7563 (mt0) REVERT: H 89 ILE cc_start: 0.8737 (mt) cc_final: 0.8393 (mp) REVERT: H 121 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8480 (mm) outliers start: 12 outliers final: 8 residues processed: 49 average time/residue: 0.5255 time to fit residues: 27.0280 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.0040 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.112879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095992 restraints weight = 5924.140| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.55 r_work: 0.3139 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.004 0.042 5685 Z= 0.158 Angle : 0.499 6.398 7908 Z= 0.282 Chirality : 0.039 0.136 876 Planarity : 0.003 0.044 832 Dihedral : 20.702 160.995 1227 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.65 % Allowed : 16.53 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.36), residues: 532 helix: 1.78 (0.35), residues: 230 sheet: -0.96 (0.51), residues: 96 loop : -0.37 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 242 TYR 0.018 0.001 TYR H 127 PHE 0.008 0.001 PHE H 190 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5685) covalent geometry : angle 0.49915 ( 7908) hydrogen bonds : bond 0.03499 ( 306) hydrogen bonds : angle 4.27401 ( 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 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.177 Fit side-chains REVERT: G 12 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8028 (mtm180) REVERT: G 23 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7774 (ptmt) REVERT: G 95 MET cc_start: 0.9097 (mtt) cc_final: 0.8738 (ttm) REVERT: H 56 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7513 (mtp180) REVERT: H 70 GLN cc_start: 0.7910 (mt0) cc_final: 0.7577 (mt0) REVERT: H 89 ILE cc_start: 0.8766 (mt) cc_final: 0.8438 (mp) REVERT: H 121 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8483 (mm) outliers start: 13 outliers final: 8 residues processed: 51 average time/residue: 0.5393 time to fit residues: 28.9165 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 ASN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094716 restraints weight = 6045.381| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.58 r_work: 0.3118 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5685 Z= 0.189 Angle : 0.527 6.453 7908 Z= 0.295 Chirality : 0.040 0.139 876 Planarity : 0.004 0.044 832 Dihedral : 20.796 160.891 1227 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.06 % Allowed : 17.35 % 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 aren not related in a simple way. whole: 0.61 (0.36), residues: 532 helix: 1.73 (0.35), residues: 232 sheet: -0.93 (0.51), residues: 96 loop : -0.37 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 39 TYR 0.026 0.001 TYR H 223 PHE 0.009 0.001 PHE H 190 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5685) covalent geometry : angle 0.52683 ( 7908) hydrogen bonds : bond 0.03688 ( 306) hydrogen bonds : angle 4.33124 ( 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.248 Fit side-chains REVERT: G 12 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8060 (mtm180) REVERT: G 23 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7771 (ptmt) REVERT: G 95 MET cc_start: 0.9107 (mtt) cc_final: 0.8746 (ttm) REVERT: H 56 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7561 (mtp180) REVERT: H 70 GLN cc_start: 0.7951 (mt0) cc_final: 0.7605 (mt0) REVERT: H 89 ILE cc_start: 0.8775 (mt) cc_final: 0.8452 (mp) REVERT: H 121 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8463 (mm) outliers start: 15 outliers final: 11 residues processed: 49 average time/residue: 0.5403 time to fit residues: 27.9187 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 : 0.199 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.113328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096285 restraints weight = 5878.242| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.55 r_work: 0.3147 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1785 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= 0.154 Angle : 0.519 10.505 7908 Z= 0.287 Chirality : 0.039 0.138 876 Planarity : 0.003 0.044 832 Dihedral : 20.692 161.147 1227 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.06 % Allowed : 18.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.36), residues: 532 helix: 1.88 (0.35), residues: 232 sheet: -0.87 (0.52), residues: 96 loop : -0.35 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 242 TYR 0.021 0.001 TYR H 223 PHE 0.008 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 covalent geometry : bond 0.00345 ( 5685) covalent geometry : angle 0.51930 ( 7908) hydrogen bonds : bond 0.03444 ( 306) hydrogen bonds : angle 4.22964 ( 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 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.205 Fit side-chains REVERT: G 12 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7993 (mtm180) REVERT: G 23 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7775 (ptmt) REVERT: G 95 MET cc_start: 0.9125 (mtt) cc_final: 0.8786 (ttm) REVERT: H 56 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7514 (mtp180) REVERT: H 70 GLN cc_start: 0.8017 (mt0) cc_final: 0.7655 (mt0) REVERT: H 89 ILE cc_start: 0.8748 (mt) cc_final: 0.8435 (mp) REVERT: H 121 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8459 (mm) REVERT: H 151 MET cc_start: 0.7331 (mmm) cc_final: 0.6415 (ptm) outliers start: 15 outliers final: 10 residues processed: 49 average time/residue: 0.5983 time to fit residues: 30.6716 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 : 0.214 ------------------------------------------------------------------------------- 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 56 ARG Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 123 GLU 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: 0.8980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 7 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.113330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.096447 restraints weight = 5861.789| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.54 r_work: 0.3148 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1834 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= 0.154 Angle : 0.517 9.208 7908 Z= 0.285 Chirality : 0.039 0.138 876 Planarity : 0.003 0.043 832 Dihedral : 20.667 160.922 1227 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.65 % Allowed : 18.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.36), residues: 532 helix: 1.92 (0.35), residues: 232 sheet: -0.83 (0.52), residues: 96 loop : -0.33 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 242 TYR 0.021 0.001 TYR H 223 PHE 0.008 0.001 PHE H 190 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5685) covalent geometry : angle 0.51656 ( 7908) hydrogen bonds : bond 0.03395 ( 306) hydrogen bonds : angle 4.20981 ( 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.182 Fit side-chains REVERT: G 12 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7991 (mtm180) REVERT: G 23 LYS cc_start: 0.8260 (ttmm) cc_final: 0.7777 (ptmt) REVERT: G 95 MET cc_start: 0.9130 (mtt) cc_final: 0.8799 (ttm) REVERT: H 56 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7517 (mtp180) REVERT: H 70 GLN cc_start: 0.8002 (mt0) cc_final: 0.7657 (mt0) REVERT: H 89 ILE cc_start: 0.8756 (mt) cc_final: 0.8444 (mp) REVERT: H 121 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8453 (mm) REVERT: H 151 MET cc_start: 0.7279 (mmm) cc_final: 0.6630 (ptm) outliers start: 13 outliers final: 10 residues processed: 47 average time/residue: 0.6454 time to fit residues: 31.6502 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 : 0.174 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.111757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094781 restraints weight = 5979.353| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.56 r_work: 0.3120 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5685 Z= 0.196 Angle : 0.539 8.863 7908 Z= 0.296 Chirality : 0.040 0.137 876 Planarity : 0.004 0.044 832 Dihedral : 20.802 160.902 1227 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.65 % Allowed : 19.18 % Favored : 78.16 % 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 aren not related in a simple way. whole: 0.76 (0.36), residues: 532 helix: 1.90 (0.35), residues: 232 sheet: -0.83 (0.52), residues: 96 loop : -0.36 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 242 TYR 0.022 0.001 TYR H 223 PHE 0.011 0.001 PHE H 190 TRP 0.013 0.001 TRP H 229 HIS 0.003 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5685) covalent geometry : angle 0.53890 ( 7908) hydrogen bonds : bond 0.03601 ( 306) hydrogen bonds : angle 4.29505 ( 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 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 Fit side-chains REVERT: G 12 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8051 (mtm180) REVERT: G 23 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7745 (ptmt) REVERT: G 95 MET cc_start: 0.9108 (mtt) cc_final: 0.8760 (ttm) REVERT: H 56 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7561 (mtp180) REVERT: H 70 GLN cc_start: 0.8016 (mt0) cc_final: 0.7663 (mt0) REVERT: H 89 ILE cc_start: 0.8770 (mt) cc_final: 0.8450 (mp) REVERT: H 121 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8455 (mm) REVERT: H 151 MET cc_start: 0.7284 (mmm) cc_final: 0.6646 (ptm) outliers start: 13 outliers final: 10 residues processed: 45 average time/residue: 0.5502 time to fit residues: 26.0719 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 : 0.196 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 0.0570 chunk 51 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.114635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097764 restraints weight = 5881.940| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.55 r_work: 0.3165 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1953 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= 0.136 Angle : 0.503 8.572 7908 Z= 0.279 Chirality : 0.039 0.136 876 Planarity : 0.003 0.043 832 Dihedral : 20.601 161.371 1227 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.24 % Allowed : 19.59 % Favored : 78.16 % 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 aren not related in a simple way. whole: 0.88 (0.36), residues: 532 helix: 1.97 (0.35), residues: 232 sheet: -0.76 (0.52), residues: 96 loop : -0.26 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 242 TYR 0.018 0.001 TYR H 223 PHE 0.009 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 covalent geometry : bond 0.00302 ( 5685) covalent geometry : angle 0.50339 ( 7908) hydrogen bonds : bond 0.03260 ( 306) hydrogen bonds : angle 4.13670 ( 884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.82 seconds wall clock time: 30 minutes 14.31 seconds (1814.31 seconds total)