Starting phenix.real_space_refine on Thu Oct 22 18:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zrt_74630/10_2026/9zrt_74630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zrt_74630/10_2026/9zrt_74630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zrt_74630/10_2026/9zrt_74630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zrt_74630/10_2026/9zrt_74630.map" model { file = "/net/cci-nas-00/data/ceres_data/9zrt_74630/10_2026/9zrt_74630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zrt_74630/10_2026/9zrt_74630.cif" } resolution = 3.3 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= 0.035 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: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2168 2.51 5 N 574 2.21 5 O 678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3433 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1727 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 216} Chain breaks: 3 Chain: "H" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "L" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Time building chain proxies: 1.06, per 1000 atoms: 0.31 Number of scatterers: 3433 At special positions: 0 Unit cell: (60.434, 84.755, 89.914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 678 8.00 N 574 7.00 C 2168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 0.26 Conformation dependent library (CDL) restraints added in 132.1 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 7 sheets defined 42.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.529A pdb=" N ILE D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 59 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 removed outlier: 3.569A pdb=" N LEU D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.877A pdb=" N ASP D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 148 Processing helix chain 'D' and resid 149 through 173 removed outlier: 3.673A pdb=" N MET D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 178 removed outlier: 3.704A pdb=" N TRP D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 219 through 231 removed outlier: 3.920A pdb=" N GLU D 229 " --> pdb=" O LYS D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 removed outlier: 3.728A pdb=" N ASN D 255 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 317 removed outlier: 3.744A pdb=" N GLN D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 307 " --> pdb=" O ASN D 303 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.666A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.086A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 210 through 213 removed outlier: 6.578A pdb=" N VAL D 246 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 12.174A pdb=" N TYR D 244 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 218 " --> pdb=" O TYR D 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 210 through 213 removed outlier: 6.578A pdb=" N VAL D 246 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 12.174A pdb=" N TYR D 244 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.684A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.897A pdb=" N TYR H 34 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP H 35 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.642A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.563A pdb=" N ASN L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1077 1.34 - 1.46: 568 1.46 - 1.57: 1829 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3495 Sorted by residual: bond pdb=" CB ASP L 28 " pdb=" CG ASP L 28 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.75e+00 bond pdb=" CB ASP D 287 " pdb=" CG ASP D 287 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.16e+00 bond pdb=" CB GLU H 16 " pdb=" CG GLU H 16 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB MET H 100C" pdb=" CG MET H 100C" ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" C THR D 251 " pdb=" N PRO D 252 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.30e-02 5.92e+03 1.26e+00 ... (remaining 3490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 4580 1.84 - 3.68: 129 3.68 - 5.52: 14 5.52 - 7.37: 8 7.37 - 9.21: 4 Bond angle restraints: 4735 Sorted by residual: angle pdb=" C PRO H 14 " pdb=" N LEU H 15 " pdb=" CA LEU H 15 " ideal model delta sigma weight residual 122.40 127.41 -5.01 1.45e+00 4.76e-01 1.19e+01 angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 113.10 109.77 3.33 9.70e-01 1.06e+00 1.18e+01 angle pdb=" CB GLU H 16 " pdb=" CG GLU H 16 " pdb=" CD GLU H 16 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.70e+00 3.46e-01 1.16e+01 angle pdb=" C GLY D 265 " pdb=" N ASN D 266 " pdb=" CA ASN D 266 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.90e+00 angle pdb=" CA TYR D 149 " pdb=" CB TYR D 149 " pdb=" CG TYR D 149 " ideal model delta sigma weight residual 113.90 119.18 -5.28 1.80e+00 3.09e-01 8.60e+00 ... (remaining 4730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 1886 16.11 - 32.21: 162 32.21 - 48.31: 47 48.31 - 64.42: 5 64.42 - 80.52: 2 Dihedral angle restraints: 2102 sinusoidal: 821 harmonic: 1281 Sorted by residual: dihedral pdb=" CA ASN H 31 " pdb=" C ASN H 31 " pdb=" N ALA H 32 " pdb=" CA ALA H 32 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLN L 89 " pdb=" C GLN L 89 " pdb=" N GLN L 90 " pdb=" CA GLN L 90 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 58.93 34.07 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 2099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 461 0.061 - 0.122: 69 0.122 - 0.183: 13 0.183 - 0.244: 0 0.244 - 0.304: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CG LEU L 33 " pdb=" CB LEU L 33 " pdb=" CD1 LEU L 33 " pdb=" CD2 LEU L 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB VAL H 67 " pdb=" CA VAL H 67 " pdb=" CG1 VAL H 67 " pdb=" CG2 VAL H 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA VAL H 12 " pdb=" N VAL H 12 " pdb=" C VAL H 12 " pdb=" CB VAL H 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 541 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " -0.044 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO L 40 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 60 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO H 61 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO L 80 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.027 5.00e-02 4.00e+02 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 973 2.81 - 3.33: 2879 3.33 - 3.86: 5508 3.86 - 4.38: 6306 4.38 - 4.90: 11236 Nonbonded interactions: 26902 Sorted by model distance: nonbonded pdb=" OH TYR D 164 " pdb=" OD1 ASP D 287 " model vdw 2.292 3.040 nonbonded pdb=" OD2 ASP D 166 " pdb=" OH TYR D 206 " model vdw 2.369 3.040 nonbonded pdb=" O ASN D 303 " pdb=" OG SER D 306 " model vdw 2.376 3.040 nonbonded pdb=" OG SER D 82 " pdb=" OE1 GLU D 154 " model vdw 2.381 3.040 nonbonded pdb=" O ASN H 100F" pdb=" ND2 ASN L 34 " model vdw 2.393 3.120 ... (remaining 26897 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.970 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.910 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.004 0.044 3497 Z= 0.178 Angle : 0.775 9.207 4739 Z= 0.419 Chirality : 0.047 0.304 544 Planarity : 0.006 0.068 599 Dihedral : 13.087 80.523 1268 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -2.53 (0.34), residues: 429 helix: -3.14 (0.21), residues: 158 sheet: 0.18 (0.57), residues: 90 loop : -1.05 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 38 TYR 0.032 0.002 TYR D 153 PHE 0.028 0.002 PHE L 98 TRP 0.030 0.002 TRP D 279 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 3495) covalent geometry : angle 0.77504 / 0.42 ( 4735) SS BOND : bond 0.00290 / 0.14 ( 2) SS BOND : angle 0.90701 / 0.76 ( 4) hydrogen bonds : bond 0.27482 / 17.41 ( 187) hydrogen bonds : angle 9.19556 / 6.29 ( 531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.144 Fit side-chains REVERT: D 149 TYR cc_start: 0.5958 (m-10) cc_final: 0.5582 (m-80) REVERT: D 286 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7591 (mp0) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0582 time to fit residues: 5.8032 Evaluate side-chains 66 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 75 ASN L 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108551 restraints weight = 5238.177| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.18 r_work: 0.3196 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3497 Z= 0.121 Angle : 0.527 8.057 4739 Z= 0.280 Chirality : 0.040 0.183 544 Planarity : 0.005 0.048 599 Dihedral : 4.220 19.197 463 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.78 % Allowed : 6.74 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.54 (0.37), residues: 429 helix: -0.20 (0.35), residues: 159 sheet: 0.45 (0.54), residues: 99 loop : -0.85 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 97 TYR 0.017 0.001 TYR D 164 PHE 0.013 0.001 PHE L 98 TRP 0.022 0.001 TRP D 279 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 3495) covalent geometry : angle 0.52715 / 0.28 ( 4735) SS BOND : bond 0.00145 / 0.07 ( 2) SS BOND : angle 0.35385 / 0.22 ( 4) hydrogen bonds : bond 0.04046 / 2.64 ( 187) hydrogen bonds : angle 4.77247 / 3.26 ( 531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.144 Fit side-chains REVERT: D 87 MET cc_start: 0.8398 (tpp) cc_final: 0.7838 (ptt) REVERT: D 149 TYR cc_start: 0.6498 (m-10) cc_final: 0.6202 (m-80) REVERT: D 250 MET cc_start: 0.7523 (mmp) cc_final: 0.7009 (mmp) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.0478 time to fit residues: 4.9411 Evaluate side-chains 71 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [39, 17, 38, 14, 0, 9, 13, 36, 26, 8, 31] chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103414 restraints weight = 5183.861| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.14 r_work: 0.3139 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3497 Z= 0.181 Angle : 0.545 7.065 4739 Z= 0.291 Chirality : 0.042 0.177 544 Planarity : 0.004 0.043 599 Dihedral : 4.263 20.276 463 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.30 % Allowed : 10.10 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.19 (0.38), residues: 429 helix: 0.92 (0.38), residues: 159 sheet: 0.45 (0.56), residues: 92 loop : -0.71 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.017 0.002 TYR D 164 PHE 0.012 0.002 PHE L 98 TRP 0.009 0.001 TRP H 100G HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 3495) covalent geometry : angle 0.54542 / 0.29 ( 4735) SS BOND : bond 0.00127 / 0.07 ( 2) SS BOND : angle 0.29513 / 0.17 ( 4) hydrogen bonds : bond 0.03694 / 2.38 ( 187) hydrogen bonds : angle 4.46002 / 3.06 ( 531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.141 Fit side-chains REVERT: D 87 MET cc_start: 0.8450 (tpp) cc_final: 0.8003 (ptt) REVERT: D 241 ASN cc_start: 0.8337 (t0) cc_final: 0.8086 (t0) REVERT: D 250 MET cc_start: 0.8096 (mmp) cc_final: 0.7744 (mmp) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.0365 time to fit residues: 3.7942 Evaluate side-chains 72 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [13, 15, 41, 14, 34, 42, 1, 3, 28, 31, 21] chunk 13 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107696 restraints weight = 5095.476| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.03 r_work: 0.3200 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3497 Z= 0.112 Angle : 0.477 5.496 4739 Z= 0.256 Chirality : 0.040 0.175 544 Planarity : 0.004 0.042 599 Dihedral : 3.908 18.027 463 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.30 % Allowed : 12.95 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.69 (0.39), residues: 429 helix: 1.55 (0.39), residues: 158 sheet: 0.66 (0.57), residues: 91 loop : -0.60 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.016 0.001 TYR D 164 PHE 0.010 0.001 PHE D 283 TRP 0.010 0.001 TRP D 226 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 3495) covalent geometry : angle 0.47680 / 0.26 ( 4735) SS BOND : bond 0.00065 / 0.03 ( 2) SS BOND : angle 0.23101 / 0.16 ( 4) hydrogen bonds : bond 0.03196 / 2.08 ( 187) hydrogen bonds : angle 4.15821 / 2.83 ( 531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 87 MET cc_start: 0.8411 (tpp) cc_final: 0.8020 (ptt) REVERT: D 149 TYR cc_start: 0.7006 (m-10) cc_final: 0.6317 (m-80) REVERT: D 241 ASN cc_start: 0.8308 (t0) cc_final: 0.8066 (t0) REVERT: D 250 MET cc_start: 0.7965 (mmp) cc_final: 0.7596 (mmp) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.0498 time to fit residues: 4.8224 Evaluate side-chains 67 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [5, 12, 32, 41, 25, 26, 20, 6, 15, 40, 11] chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103273 restraints weight = 5243.287| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.15 r_work: 0.3105 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3497 Z= 0.145 Angle : 0.506 5.638 4739 Z= 0.272 Chirality : 0.041 0.184 544 Planarity : 0.004 0.041 599 Dihedral : 4.014 18.617 463 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.30 % Allowed : 14.25 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.80 (0.39), residues: 429 helix: 1.68 (0.39), residues: 158 sheet: 0.66 (0.57), residues: 91 loop : -0.54 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.019 0.002 TYR D 164 PHE 0.009 0.001 PHE D 283 TRP 0.008 0.001 TRP D 226 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 3495) covalent geometry : angle 0.50601 / 0.27 ( 4735) SS BOND : bond 0.00063 / 0.03 ( 2) SS BOND : angle 0.18453 / 0.10 ( 4) hydrogen bonds : bond 0.03253 / 2.12 ( 187) hydrogen bonds : angle 4.09492 / 2.80 ( 531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: D 87 MET cc_start: 0.8415 (tpp) cc_final: 0.8042 (ptt) REVERT: D 241 ASN cc_start: 0.8289 (t0) cc_final: 0.8049 (t0) REVERT: D 250 MET cc_start: 0.8155 (mmp) cc_final: 0.7946 (mmp) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.0427 time to fit residues: 4.3708 Evaluate side-chains 69 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [35, 39, 34, 27, 3, 17, 20, 2, 1, 30, 25] chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 293 ASN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102918 restraints weight = 5207.386| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.14 r_work: 0.3098 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3497 Z= 0.149 Angle : 0.504 5.765 4739 Z= 0.273 Chirality : 0.041 0.193 544 Planarity : 0.004 0.041 599 Dihedral : 4.018 18.846 463 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.85 % Allowed : 14.51 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.91 (0.40), residues: 429 helix: 1.83 (0.39), residues: 158 sheet: 0.57 (0.57), residues: 92 loop : -0.45 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.023 0.002 TYR D 164 PHE 0.009 0.001 PHE D 283 TRP 0.018 0.001 TRP D 226 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3495) covalent geometry : angle 0.50432 / 0.27 ( 4735) SS BOND : bond 0.00053 / 0.03 ( 2) SS BOND : angle 0.20548 / 0.13 ( 4) hydrogen bonds : bond 0.03215 / 2.09 ( 187) hydrogen bonds : angle 4.08429 / 2.79 ( 531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: D 87 MET cc_start: 0.8430 (tpp) cc_final: 0.8070 (ptt) REVERT: D 149 TYR cc_start: 0.6672 (m-10) cc_final: 0.6408 (m-80) REVERT: D 241 ASN cc_start: 0.8274 (t0) cc_final: 0.8027 (t0) REVERT: D 250 MET cc_start: 0.8146 (mmp) cc_final: 0.7945 (mmp) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.0511 time to fit residues: 5.0446 Evaluate side-chains 72 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [26, 40, 16, 5, 38, 36, 18, 8, 10, 24, 2] chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100589 restraints weight = 5226.634| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.14 r_work: 0.3056 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3497 Z= 0.192 Angle : 0.555 6.111 4739 Z= 0.299 Chirality : 0.042 0.200 544 Planarity : 0.004 0.041 599 Dihedral : 4.198 20.171 463 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.85 % Allowed : 15.28 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.85 (0.40), residues: 429 helix: 1.73 (0.39), residues: 158 sheet: 0.51 (0.57), residues: 92 loop : -0.42 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.029 0.002 TYR D 164 PHE 0.011 0.002 PHE D 167 TRP 0.017 0.002 TRP D 226 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 3495) covalent geometry : angle 0.55548 / 0.30 ( 4735) SS BOND : bond 0.00142 / 0.07 ( 2) SS BOND : angle 0.20154 / 0.09 ( 4) hydrogen bonds : bond 0.03429 / 2.23 ( 187) hydrogen bonds : angle 4.19547 / 2.88 ( 531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: D 87 MET cc_start: 0.8437 (tpp) cc_final: 0.8042 (ptt) REVERT: D 241 ASN cc_start: 0.8279 (t0) cc_final: 0.8049 (t0) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.0451 time to fit residues: 4.6377 Evaluate side-chains 74 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [20, 21, 13, 1, 35, 26, 36, 33, 3, 24, 30] chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102192 restraints weight = 5220.873| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.15 r_work: 0.3126 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3497 Z= 0.146 Angle : 0.520 6.124 4739 Z= 0.282 Chirality : 0.041 0.190 544 Planarity : 0.004 0.041 599 Dihedral : 3.990 18.973 463 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 17.10 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.81 (0.40), residues: 429 helix: 1.85 (0.39), residues: 157 sheet: 0.52 (0.57), residues: 92 loop : -0.60 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.028 0.002 TYR D 164 PHE 0.008 0.001 PHE D 283 TRP 0.012 0.001 TRP D 226 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 3495) covalent geometry : angle 0.52050 / 0.28 ( 4735) SS BOND : bond 0.00036 / 0.02 ( 2) SS BOND : angle 0.22242 / 0.14 ( 4) hydrogen bonds : bond 0.03271 / 2.16 ( 187) hydrogen bonds : angle 4.06184 / 2.77 ( 531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: D 87 MET cc_start: 0.8475 (tpp) cc_final: 0.8075 (ptt) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.0475 time to fit residues: 4.6289 Evaluate side-chains 72 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [5, 26, 34, 18, 22, 7, 42, 1, 30, 15, 20] chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101978 restraints weight = 5155.277| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.18 r_work: 0.3101 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3497 Z= 0.156 Angle : 0.535 5.338 4739 Z= 0.291 Chirality : 0.041 0.195 544 Planarity : 0.004 0.041 599 Dihedral : 4.014 18.713 463 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 17.36 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 (0.40), residues: 429 helix: 1.75 (0.39), residues: 158 sheet: 0.53 (0.57), residues: 92 loop : -0.57 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.022 0.002 TYR D 164 PHE 0.007 0.001 PHE D 283 TRP 0.016 0.001 TRP D 226 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 3495) covalent geometry : angle 0.53527 / 0.29 ( 4735) SS BOND : bond 0.00056 / 0.03 ( 2) SS BOND : angle 0.20665 / 0.11 ( 4) hydrogen bonds : bond 0.03259 / 2.14 ( 187) hydrogen bonds : angle 4.08512 / 2.81 ( 531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: D 87 MET cc_start: 0.8450 (tpp) cc_final: 0.8075 (ptt) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.0416 time to fit residues: 3.9859 Evaluate side-chains 72 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [13, 10, 21, 1, 31, 6, 15, 25, 23, 26, 28] chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103695 restraints weight = 5161.649| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.09 r_work: 0.3094 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3497 Z= 0.141 Angle : 0.525 5.018 4739 Z= 0.285 Chirality : 0.041 0.194 544 Planarity : 0.004 0.041 599 Dihedral : 3.962 18.037 463 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.81 % Allowed : 17.88 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.74 (0.40), residues: 429 helix: 1.85 (0.40), residues: 157 sheet: 0.66 (0.57), residues: 91 loop : -0.81 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.022 0.002 TYR D 164 PHE 0.008 0.001 PHE D 283 TRP 0.014 0.001 TRP D 226 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3495) covalent geometry : angle 0.52483 / 0.29 ( 4735) SS BOND : bond 0.00034 / 0.02 ( 2) SS BOND : angle 0.32744 / 0.21 ( 4) hydrogen bonds : bond 0.03236 / 2.14 ( 187) hydrogen bonds : angle 4.05390 / 2.78 ( 531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: D 87 MET cc_start: 0.8452 (tpp) cc_final: 0.8068 (ptt) REVERT: D 148 GLN cc_start: 0.7669 (tp40) cc_final: 0.6496 (mm-40) outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.0386 time to fit residues: 3.4947 Evaluate side-chains 67 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: [1, 11, 29, 22, 36, 15, 21, 16, 0, 17, 31] chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.139779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104011 restraints weight = 5183.862| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.06 r_work: 0.3094 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3497 Z= 0.152 Angle : 0.532 5.059 4739 Z= 0.288 Chirality : 0.041 0.199 544 Planarity : 0.004 0.041 599 Dihedral : 3.992 18.033 463 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.81 % Allowed : 17.88 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 (0.40), residues: 429 helix: 1.78 (0.40), residues: 158 sheet: 0.53 (0.57), residues: 92 loop : -0.62 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.022 0.002 TYR D 164 PHE 0.007 0.001 PHE D 283 TRP 0.013 0.001 TRP D 226 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 3495) covalent geometry : angle 0.53214 / 0.29 ( 4735) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 0.23727 / 0.16 ( 4) hydrogen bonds : bond 0.03216 / 2.10 ( 187) hydrogen bonds : angle 4.09985 / 2.84 ( 531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1199.86 seconds wall clock time: 21 minutes 18.11 seconds (1278.11 seconds total)