Starting phenix.real_space_refine on Fri May 9 18:27:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5e_37287/05_2025/8w5e_37287.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5e_37287/05_2025/8w5e_37287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5e_37287/05_2025/8w5e_37287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5e_37287/05_2025/8w5e_37287.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5e_37287/05_2025/8w5e_37287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5e_37287/05_2025/8w5e_37287.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.119 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 11 5.16 5 C 2128 2.51 5 N 575 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3396 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 782 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 944 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Restraints were copied for chains: c Time building chain proxies: 2.82, per 1000 atoms: 0.83 Number of scatterers: 3396 At special positions: 0 Unit cell: (91.8, 66.15, 85.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 2 15.00 O 680 8.00 N 575 7.00 C 2128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " 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: 0.76 Conformation dependent library (CDL) restraints added in 372.9 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 10.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'c' and resid 101 through 116 removed outlier: 3.884A pdb=" N VAL c 108 " --> pdb=" O GLU c 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG c 109 " --> pdb=" O ARG c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 126 removed outlier: 3.533A pdb=" N ASP c 126 " --> pdb=" O ILE c 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.885A pdb=" N VAL C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.533A pdb=" N ASP C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.729A pdb=" N ASN H 80 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 37 through 39 removed outlier: 3.824A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 22 through 27 removed outlier: 4.996A pdb=" N SER c 34 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL c 26 " --> pdb=" O VAL c 32 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL c 32 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN c 70 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG c 86 " --> pdb=" O THR c 72 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N CYS c 74 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL c 84 " --> pdb=" O CYS c 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 22 through 27 removed outlier: 4.996A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.799A pdb=" N ASP L 88 " --> pdb=" O GLN L 41 " (cutoff:3.500A) 99 hydrogen bonds defined for protein. 264 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: 0.76 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 973 1.33 - 1.45: 599 1.45 - 1.57: 1863 1.57 - 1.70: 8 1.70 - 1.82: 14 Bond restraints: 3457 Sorted by residual: bond pdb=" C VAL H 8 " pdb=" O VAL H 8 " ideal model delta sigma weight residual 1.237 1.212 0.024 1.07e-02 8.73e+03 5.08e+00 bond pdb=" CA VAL H 8 " pdb=" CB VAL H 8 " ideal model delta sigma weight residual 1.540 1.513 0.028 1.23e-02 6.61e+03 5.01e+00 bond pdb=" CA SER H 10 " pdb=" CB SER H 10 " ideal model delta sigma weight residual 1.534 1.500 0.033 1.78e-02 3.16e+03 3.50e+00 bond pdb=" C SER H 10 " pdb=" O SER H 10 " ideal model delta sigma weight residual 1.234 1.212 0.022 1.22e-02 6.72e+03 3.37e+00 bond pdb=" N THR L 81 " pdb=" CA THR L 81 " ideal model delta sigma weight residual 1.460 1.486 -0.027 1.54e-02 4.22e+03 3.02e+00 ... (remaining 3452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 4560 2.81 - 5.61: 117 5.61 - 8.42: 23 8.42 - 11.22: 5 11.22 - 14.03: 4 Bond angle restraints: 4709 Sorted by residual: angle pdb=" N VAL H 8 " pdb=" CA VAL H 8 " pdb=" C VAL H 8 " ideal model delta sigma weight residual 108.11 122.14 -14.03 1.40e+00 5.10e-01 1.00e+02 angle pdb=" N VAL H 8 " pdb=" CA VAL H 8 " pdb=" CB VAL H 8 " ideal model delta sigma weight residual 111.41 104.80 6.61 1.38e+00 5.25e-01 2.29e+01 angle pdb=" N ILE L 51 " pdb=" CA ILE L 51 " pdb=" C ILE L 51 " ideal model delta sigma weight residual 109.34 119.25 -9.91 2.08e+00 2.31e-01 2.27e+01 angle pdb=" C LEU L 50 " pdb=" N ILE L 51 " pdb=" CA ILE L 51 " ideal model delta sigma weight residual 121.97 130.29 -8.32 1.80e+00 3.09e-01 2.14e+01 angle pdb=" C VAL H 8 " pdb=" CA VAL H 8 " pdb=" CB VAL H 8 " ideal model delta sigma weight residual 110.63 103.90 6.73 1.48e+00 4.57e-01 2.07e+01 ... (remaining 4704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 1970 15.23 - 30.46: 83 30.46 - 45.69: 24 45.69 - 60.92: 7 60.92 - 76.14: 4 Dihedral angle restraints: 2088 sinusoidal: 799 harmonic: 1289 Sorted by residual: dihedral pdb=" CA LEU L 50 " pdb=" C LEU L 50 " pdb=" N ILE L 51 " pdb=" CA ILE L 51 " ideal model delta harmonic sigma weight residual -180.00 -149.45 -30.55 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA ASN L 96 " pdb=" C ASN L 96 " pdb=" N MET L 97 " pdb=" CA MET L 97 " ideal model delta harmonic sigma weight residual -180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ILE L 78 " pdb=" C ILE L 78 " pdb=" N GLU L 79 " pdb=" CA GLU L 79 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 332 0.048 - 0.096: 144 0.096 - 0.145: 52 0.145 - 0.193: 15 0.193 - 0.241: 4 Chirality restraints: 547 Sorted by residual: chirality pdb=" CB ILE c 68 " pdb=" CA ILE c 68 " pdb=" CG1 ILE c 68 " pdb=" CG2 ILE c 68 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE C 68 " pdb=" CA ILE C 68 " pdb=" CG1 ILE C 68 " pdb=" CG2 ILE C 68 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL L 61 " pdb=" CA VAL L 61 " pdb=" CG1 VAL L 61 " pdb=" CG2 VAL L 61 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 544 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE L 78 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C ILE L 78 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE L 78 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU L 79 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN c 70 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO c 71 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO c 71 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO c 71 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 70 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO C 71 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 71 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 71 " -0.028 5.00e-02 4.00e+02 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 38 2.61 - 3.19: 2878 3.19 - 3.76: 4920 3.76 - 4.33: 6298 4.33 - 4.90: 10746 Nonbonded interactions: 24880 Sorted by model distance: nonbonded pdb=" SG CYS L 26 " pdb=" SG CYS L 91 " model vdw 2.042 3.760 nonbonded pdb=" OE1 GLU H 9 " pdb=" C ARG H 115 " model vdw 2.158 3.270 nonbonded pdb=" OD1 ASP c 91 " pdb=" OG1 THR C 93 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR c 93 " pdb=" OD1 ASP C 91 " model vdw 2.298 3.040 nonbonded pdb=" O SER L 52 " pdb=" OG1 THR L 56 " model vdw 2.318 3.040 ... (remaining 24875 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 'C' selection = chain 'c' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.760 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.007 0.039 3458 Z= 0.317 Angle : 1.177 14.027 4711 Z= 0.621 Chirality : 0.064 0.241 547 Planarity : 0.008 0.051 612 Dihedral : 11.145 76.144 1253 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.86 % Favored : 89.67 % Rotamer: Outliers : 0.54 % Allowed : 5.91 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.34), residues: 426 helix: -3.63 (0.59), residues: 44 sheet: -2.33 (0.39), residues: 158 loop : -3.50 (0.32), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 113 PHE 0.021 0.003 PHE H 110 TYR 0.022 0.003 TYR c 62 ARG 0.005 0.001 ARG C 109 Details of bonding type rmsd hydrogen bonds : bond 0.14312 ( 99) hydrogen bonds : angle 7.14855 ( 264) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.79572 ( 2) covalent geometry : bond 0.00675 ( 3457) covalent geometry : angle 1.17757 ( 4709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: H 41 ARG cc_start: 0.6838 (ptp-170) cc_final: 0.5625 (mmm160) REVERT: H 55 SER cc_start: 0.9381 (t) cc_final: 0.9087 (t) REVERT: H 80 ASN cc_start: 0.8341 (p0) cc_final: 0.8121 (p0) REVERT: H 101 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7852 (ptt90) REVERT: H 106 SER cc_start: 0.8089 (t) cc_final: 0.7331 (t) REVERT: c 13 LYS cc_start: 0.8920 (tppp) cc_final: 0.7829 (tppp) REVERT: c 27 ASN cc_start: 0.8595 (t0) cc_final: 0.8182 (t0) REVERT: c 32 VAL cc_start: 0.9273 (t) cc_final: 0.9021 (m) REVERT: c 34 SER cc_start: 0.9509 (m) cc_final: 0.9063 (t) REVERT: c 87 GLN cc_start: 0.8429 (mp-120) cc_final: 0.8206 (mm-40) REVERT: c 100 SER cc_start: 0.9434 (m) cc_final: 0.9150 (p) REVERT: c 103 GLU cc_start: 0.8355 (tp30) cc_final: 0.8146 (mm-30) REVERT: c 122 ILE cc_start: 0.9094 (pp) cc_final: 0.8707 (pp) REVERT: c 123 ASP cc_start: 0.7901 (t70) cc_final: 0.7489 (t0) REVERT: C 13 LYS cc_start: 0.8795 (tppp) cc_final: 0.8400 (tppp) REVERT: C 34 SER cc_start: 0.9452 (m) cc_final: 0.9030 (p) REVERT: C 36 SER cc_start: 0.8738 (p) cc_final: 0.8414 (p) REVERT: C 91 ASP cc_start: 0.8553 (p0) cc_final: 0.8344 (p0) REVERT: C 104 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 122 ILE cc_start: 0.8522 (pp) cc_final: 0.8299 (tt) REVERT: C 123 ASP cc_start: 0.8563 (t70) cc_final: 0.7670 (t0) REVERT: C 127 GLN cc_start: 0.9275 (mp10) cc_final: 0.8690 (mp-120) REVERT: C 129 ASN cc_start: 0.8495 (m-40) cc_final: 0.8094 (m110) REVERT: L 9 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8105 (mp10) REVERT: L 13 SER cc_start: 0.7775 (m) cc_final: 0.7295 (p) REVERT: L 27 ILE cc_start: 0.8314 (tt) cc_final: 0.7936 (tt) REVERT: L 35 ASP cc_start: 0.7146 (m-30) cc_final: 0.6701 (m-30) REVERT: L 45 GLU cc_start: 0.8116 (pm20) cc_final: 0.7533 (pm20) REVERT: L 93 GLN cc_start: 0.8762 (pm20) cc_final: 0.8381 (pm20) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.1789 time to fit residues: 38.1142 Evaluate side-chains 140 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 67 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.103570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.083705 restraints weight = 7449.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086187 restraints weight = 3422.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087738 restraints weight = 2023.836| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3458 Z= 0.198 Angle : 0.825 9.767 4711 Z= 0.418 Chirality : 0.049 0.175 547 Planarity : 0.006 0.052 612 Dihedral : 5.709 25.818 483 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.09 % Favored : 89.67 % Rotamer: Outliers : 6.99 % Allowed : 13.98 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.36), residues: 426 helix: -2.12 (0.69), residues: 46 sheet: -2.26 (0.40), residues: 151 loop : -3.10 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 113 PHE 0.015 0.002 PHE L 74 TYR 0.017 0.002 TYR L 39 ARG 0.003 0.001 ARG H 75 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 99) hydrogen bonds : angle 5.86557 ( 264) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.56174 ( 2) covalent geometry : bond 0.00439 ( 3457) covalent geometry : angle 0.82558 ( 4709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ARG cc_start: 0.7604 (ptp-170) cc_final: 0.6009 (mmm160) REVERT: H 45 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.7940 (mmp-170) REVERT: H 54 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8167 (tp) REVERT: H 55 SER cc_start: 0.9162 (t) cc_final: 0.8910 (t) REVERT: H 62 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6415 (p90) REVERT: H 79 LYS cc_start: 0.8773 (mttt) cc_final: 0.8504 (ptmt) REVERT: H 105 ASP cc_start: 0.8751 (m-30) cc_final: 0.8512 (m-30) REVERT: H 112 TYR cc_start: 0.8865 (m-80) cc_final: 0.8639 (m-10) REVERT: c 4 GLU cc_start: 0.7904 (tp30) cc_final: 0.7652 (tp30) REVERT: c 6 VAL cc_start: 0.9170 (t) cc_final: 0.8952 (p) REVERT: c 13 LYS cc_start: 0.9254 (tppp) cc_final: 0.8978 (tppp) REVERT: c 24 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.8042 (mmt180) REVERT: c 27 ASN cc_start: 0.8835 (t0) cc_final: 0.8279 (t0) REVERT: c 87 GLN cc_start: 0.8318 (mp-120) cc_final: 0.8050 (mm-40) REVERT: c 100 SER cc_start: 0.9630 (m) cc_final: 0.9317 (p) REVERT: c 122 ILE cc_start: 0.9111 (pp) cc_final: 0.8814 (pp) REVERT: c 123 ASP cc_start: 0.7939 (t70) cc_final: 0.7535 (t0) REVERT: C 87 GLN cc_start: 0.8968 (mp10) cc_final: 0.8702 (mt0) REVERT: C 91 ASP cc_start: 0.8802 (p0) cc_final: 0.8595 (p0) REVERT: C 122 ILE cc_start: 0.8829 (pp) cc_final: 0.8606 (tt) REVERT: C 123 ASP cc_start: 0.8649 (t70) cc_final: 0.7800 (t0) REVERT: C 127 GLN cc_start: 0.9350 (mp10) cc_final: 0.8828 (mp-120) REVERT: C 129 ASN cc_start: 0.8620 (m-40) cc_final: 0.8185 (m110) REVERT: L 9 GLN cc_start: 0.8234 (tp-100) cc_final: 0.8016 (mp10) REVERT: L 13 SER cc_start: 0.7450 (m) cc_final: 0.7023 (p) REVERT: L 45 GLU cc_start: 0.8137 (pm20) cc_final: 0.7569 (pm20) REVERT: L 70 TYR cc_start: 0.7708 (t80) cc_final: 0.7075 (t80) REVERT: L 74 PHE cc_start: 0.8606 (m-80) cc_final: 0.8306 (m-10) REVERT: L 93 GLN cc_start: 0.9006 (pm20) cc_final: 0.8710 (pm20) outliers start: 26 outliers final: 19 residues processed: 154 average time/residue: 0.1729 time to fit residues: 31.2221 Evaluate side-chains 147 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 53 SER Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.081192 restraints weight = 7335.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.083576 restraints weight = 3452.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085086 restraints weight = 2100.358| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3458 Z= 0.236 Angle : 0.835 13.289 4711 Z= 0.419 Chirality : 0.049 0.178 547 Planarity : 0.005 0.043 612 Dihedral : 5.463 23.126 483 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.74 % Favored : 88.03 % Rotamer: Outliers : 7.26 % Allowed : 19.09 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.36), residues: 426 helix: -1.84 (0.68), residues: 46 sheet: -2.15 (0.40), residues: 155 loop : -3.11 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 113 PHE 0.015 0.002 PHE H 53 TYR 0.013 0.002 TYR L 89 ARG 0.004 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 99) hydrogen bonds : angle 5.66088 ( 264) SS BOND : bond 0.00118 ( 1) SS BOND : angle 0.49628 ( 2) covalent geometry : bond 0.00531 ( 3457) covalent geometry : angle 0.83552 ( 4709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8415 (ttmm) REVERT: H 32 PHE cc_start: 0.8963 (t80) cc_final: 0.8750 (t80) REVERT: H 35 TYR cc_start: 0.8750 (m-80) cc_final: 0.8514 (m-80) REVERT: H 40 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7985 (p) REVERT: H 41 ARG cc_start: 0.7731 (ptp-170) cc_final: 0.6026 (mmm160) REVERT: H 53 PHE cc_start: 0.8827 (t80) cc_final: 0.8626 (t80) REVERT: H 54 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8282 (tp) REVERT: H 55 SER cc_start: 0.9181 (t) cc_final: 0.8852 (t) REVERT: H 62 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6515 (p90) REVERT: H 79 LYS cc_start: 0.8766 (mttt) cc_final: 0.8296 (ptmt) REVERT: H 112 TYR cc_start: 0.8861 (m-80) cc_final: 0.8657 (m-10) REVERT: c 4 GLU cc_start: 0.8008 (tp30) cc_final: 0.7764 (tp30) REVERT: c 27 ASN cc_start: 0.8891 (t0) cc_final: 0.8382 (t0) REVERT: c 70 ASN cc_start: 0.8640 (m-40) cc_final: 0.8316 (m-40) REVERT: c 87 GLN cc_start: 0.8326 (mp-120) cc_final: 0.8008 (mm-40) REVERT: c 103 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8133 (mm-30) REVERT: c 123 ASP cc_start: 0.8148 (t70) cc_final: 0.7712 (t0) REVERT: C 13 LYS cc_start: 0.9006 (tttp) cc_final: 0.8788 (ttmm) REVERT: C 30 ASN cc_start: 0.9282 (p0) cc_final: 0.9046 (p0) REVERT: C 87 GLN cc_start: 0.8918 (mp10) cc_final: 0.8703 (mt0) REVERT: C 122 ILE cc_start: 0.8907 (pp) cc_final: 0.8607 (tt) REVERT: C 123 ASP cc_start: 0.8743 (t70) cc_final: 0.7854 (t0) REVERT: C 127 GLN cc_start: 0.9374 (mp10) cc_final: 0.8868 (mp-120) REVERT: C 129 ASN cc_start: 0.8576 (m-40) cc_final: 0.7995 (m110) REVERT: L 13 SER cc_start: 0.7377 (m) cc_final: 0.6912 (p) REVERT: L 45 GLU cc_start: 0.8216 (pm20) cc_final: 0.7747 (pm20) outliers start: 27 outliers final: 17 residues processed: 140 average time/residue: 0.1749 time to fit residues: 28.7431 Evaluate side-chains 135 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 88 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 0.0030 overall best weight: 3.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081947 restraints weight = 7442.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.084397 restraints weight = 3429.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085948 restraints weight = 2045.074| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3458 Z= 0.190 Angle : 0.807 13.570 4711 Z= 0.402 Chirality : 0.049 0.173 547 Planarity : 0.005 0.038 612 Dihedral : 5.323 23.175 483 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.74 % Favored : 88.03 % Rotamer: Outliers : 6.99 % Allowed : 20.43 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.36), residues: 426 helix: -1.55 (0.71), residues: 46 sheet: -2.09 (0.40), residues: 155 loop : -3.00 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 113 PHE 0.007 0.001 PHE H 108 TYR 0.013 0.002 TYR L 90 ARG 0.003 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 99) hydrogen bonds : angle 5.52292 ( 264) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.40541 ( 2) covalent geometry : bond 0.00432 ( 3457) covalent geometry : angle 0.80714 ( 4709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8453 (ttmm) REVERT: H 32 PHE cc_start: 0.8935 (t80) cc_final: 0.8720 (t80) REVERT: H 40 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7910 (p) REVERT: H 41 ARG cc_start: 0.7699 (ptp-170) cc_final: 0.5996 (mmm160) REVERT: H 62 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.6547 (p90) REVERT: H 79 LYS cc_start: 0.8706 (mttt) cc_final: 0.8436 (ptmt) REVERT: c 4 GLU cc_start: 0.7988 (tp30) cc_final: 0.7746 (tp30) REVERT: c 27 ASN cc_start: 0.8784 (t0) cc_final: 0.8289 (t0) REVERT: c 87 GLN cc_start: 0.8247 (mp-120) cc_final: 0.7987 (mm-40) REVERT: c 103 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8065 (mm-30) REVERT: c 123 ASP cc_start: 0.8198 (t70) cc_final: 0.7724 (t0) REVERT: C 122 ILE cc_start: 0.8941 (pp) cc_final: 0.8646 (tt) REVERT: C 123 ASP cc_start: 0.8772 (t70) cc_final: 0.7832 (t0) REVERT: C 127 GLN cc_start: 0.9370 (mp10) cc_final: 0.8904 (mp-120) REVERT: C 129 ASN cc_start: 0.8710 (m-40) cc_final: 0.8138 (m110) REVERT: L 13 SER cc_start: 0.7225 (m) cc_final: 0.6788 (p) REVERT: L 36 MET cc_start: 0.7481 (tpt) cc_final: 0.7254 (tpt) REVERT: L 45 GLU cc_start: 0.8280 (pm20) cc_final: 0.7785 (pm20) REVERT: L 50 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8711 (mm) outliers start: 26 outliers final: 20 residues processed: 135 average time/residue: 0.1613 time to fit residues: 25.9815 Evaluate side-chains 143 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 33 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.102821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082190 restraints weight = 7483.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084674 restraints weight = 3521.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086252 restraints weight = 2125.793| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3458 Z= 0.155 Angle : 0.779 13.461 4711 Z= 0.389 Chirality : 0.048 0.167 547 Planarity : 0.005 0.037 612 Dihedral : 5.164 23.271 483 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.50 % Favored : 88.26 % Rotamer: Outliers : 7.80 % Allowed : 21.24 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.38), residues: 426 helix: -1.25 (0.79), residues: 44 sheet: -1.87 (0.40), residues: 158 loop : -2.78 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 39 PHE 0.016 0.001 PHE c 94 TYR 0.013 0.002 TYR L 90 ARG 0.002 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 99) hydrogen bonds : angle 5.38699 ( 264) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.36746 ( 2) covalent geometry : bond 0.00351 ( 3457) covalent geometry : angle 0.77870 ( 4709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8762 (m) cc_final: 0.8511 (p) REVERT: H 22 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8467 (ttmm) REVERT: H 32 PHE cc_start: 0.8913 (t80) cc_final: 0.8694 (t80) REVERT: H 41 ARG cc_start: 0.7680 (ptp-170) cc_final: 0.5991 (mmm160) REVERT: H 54 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8141 (tp) REVERT: H 62 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.6227 (p90) REVERT: H 79 LYS cc_start: 0.8708 (mttt) cc_final: 0.8345 (ptmt) REVERT: c 27 ASN cc_start: 0.8763 (t0) cc_final: 0.8272 (t0) REVERT: c 102 ASP cc_start: 0.8113 (t70) cc_final: 0.7897 (t0) REVERT: c 103 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8089 (mm-30) REVERT: c 123 ASP cc_start: 0.8131 (t70) cc_final: 0.7633 (t0) REVERT: C 13 LYS cc_start: 0.9002 (tttp) cc_final: 0.8585 (ttmm) REVERT: C 30 ASN cc_start: 0.9286 (p0) cc_final: 0.9086 (p0) REVERT: C 122 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8663 (tt) REVERT: C 123 ASP cc_start: 0.8699 (t70) cc_final: 0.7765 (t0) REVERT: C 127 GLN cc_start: 0.9380 (mp10) cc_final: 0.8923 (mp-120) REVERT: C 129 ASN cc_start: 0.8668 (m-40) cc_final: 0.8123 (m110) REVERT: L 13 SER cc_start: 0.7225 (m) cc_final: 0.6809 (p) REVERT: L 45 GLU cc_start: 0.8314 (pm20) cc_final: 0.7796 (pm20) REVERT: L 50 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8543 (mm) REVERT: L 93 GLN cc_start: 0.8996 (pm20) cc_final: 0.8776 (pm20) REVERT: L 97 MET cc_start: 0.7766 (mmm) cc_final: 0.5290 (mmm) outliers start: 29 outliers final: 17 residues processed: 143 average time/residue: 0.1586 time to fit residues: 27.0060 Evaluate side-chains 145 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081255 restraints weight = 7623.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.083718 restraints weight = 3571.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085296 restraints weight = 2144.458| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3458 Z= 0.175 Angle : 0.794 13.894 4711 Z= 0.393 Chirality : 0.048 0.161 547 Planarity : 0.005 0.040 612 Dihedral : 5.177 23.011 483 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 8.06 % Allowed : 21.51 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.38), residues: 426 helix: -1.51 (0.75), residues: 48 sheet: -1.83 (0.40), residues: 158 loop : -2.78 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 113 PHE 0.014 0.001 PHE c 94 TYR 0.023 0.002 TYR H 35 ARG 0.002 0.000 ARG c 86 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 99) hydrogen bonds : angle 5.32868 ( 264) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.43407 ( 2) covalent geometry : bond 0.00397 ( 3457) covalent geometry : angle 0.79421 ( 4709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8782 (m) cc_final: 0.8486 (p) REVERT: H 22 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8476 (ttmm) REVERT: H 41 ARG cc_start: 0.7462 (ptp-170) cc_final: 0.5790 (mmm160) REVERT: H 79 LYS cc_start: 0.8727 (mttt) cc_final: 0.8480 (ptmt) REVERT: H 111 ASP cc_start: 0.9071 (p0) cc_final: 0.8783 (p0) REVERT: c 27 ASN cc_start: 0.8758 (t0) cc_final: 0.8279 (t0) REVERT: c 87 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7433 (mm-40) REVERT: c 102 ASP cc_start: 0.8130 (t70) cc_final: 0.7653 (t0) REVERT: c 103 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7574 (mm-30) REVERT: c 123 ASP cc_start: 0.7985 (t70) cc_final: 0.7506 (t0) REVERT: C 13 LYS cc_start: 0.9048 (tttp) cc_final: 0.8265 (ttpt) REVERT: C 122 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8827 (tt) REVERT: C 123 ASP cc_start: 0.8755 (t70) cc_final: 0.7809 (t0) REVERT: C 127 GLN cc_start: 0.9397 (mp10) cc_final: 0.8930 (mp-120) REVERT: C 129 ASN cc_start: 0.8702 (m-40) cc_final: 0.8167 (m110) REVERT: L 13 SER cc_start: 0.7269 (m) cc_final: 0.6855 (p) REVERT: L 20 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: L 45 GLU cc_start: 0.8274 (pm20) cc_final: 0.7753 (pm20) REVERT: L 50 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8534 (mm) REVERT: L 97 MET cc_start: 0.7871 (mmm) cc_final: 0.7615 (tpt) outliers start: 30 outliers final: 21 residues processed: 140 average time/residue: 0.1657 time to fit residues: 27.4255 Evaluate side-chains 149 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.0050 chunk 9 optimal weight: 0.0270 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 overall best weight: 0.5252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084886 restraints weight = 7428.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087378 restraints weight = 3425.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088974 restraints weight = 2018.111| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3458 Z= 0.124 Angle : 0.763 11.309 4711 Z= 0.380 Chirality : 0.047 0.157 547 Planarity : 0.004 0.038 612 Dihedral : 4.956 23.025 483 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.92 % Favored : 90.85 % Rotamer: Outliers : 5.91 % Allowed : 24.19 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.38), residues: 426 helix: -1.20 (0.79), residues: 48 sheet: -1.61 (0.41), residues: 158 loop : -2.74 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 PHE 0.012 0.001 PHE H 32 TYR 0.019 0.001 TYR H 35 ARG 0.002 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 99) hydrogen bonds : angle 5.15497 ( 264) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.24997 ( 2) covalent geometry : bond 0.00265 ( 3457) covalent geometry : angle 0.76287 ( 4709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8740 (m) cc_final: 0.8455 (p) REVERT: H 41 ARG cc_start: 0.7445 (ptp-170) cc_final: 0.5780 (mmm160) REVERT: c 27 ASN cc_start: 0.8695 (t0) cc_final: 0.8177 (t0) REVERT: c 65 GLN cc_start: 0.7690 (pt0) cc_final: 0.7453 (tt0) REVERT: c 87 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7537 (mm-40) REVERT: c 103 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7865 (mm-30) REVERT: c 122 ILE cc_start: 0.8865 (pp) cc_final: 0.8431 (mm) REVERT: c 123 ASP cc_start: 0.7885 (t70) cc_final: 0.7318 (t0) REVERT: C 13 LYS cc_start: 0.8995 (tttp) cc_final: 0.8418 (ttmt) REVERT: C 123 ASP cc_start: 0.8674 (t70) cc_final: 0.7655 (t0) REVERT: C 127 GLN cc_start: 0.9393 (mp10) cc_final: 0.8931 (mp-120) REVERT: C 129 ASN cc_start: 0.8585 (m-40) cc_final: 0.8044 (m110) REVERT: L 13 SER cc_start: 0.7380 (m) cc_final: 0.7011 (p) REVERT: L 20 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: L 50 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8387 (mm) REVERT: L 70 TYR cc_start: 0.7776 (t80) cc_final: 0.7501 (t80) REVERT: L 93 GLN cc_start: 0.8864 (pm20) cc_final: 0.8625 (pm20) REVERT: L 97 MET cc_start: 0.7634 (mmm) cc_final: 0.7404 (tpt) outliers start: 22 outliers final: 15 residues processed: 146 average time/residue: 0.1580 time to fit residues: 27.4860 Evaluate side-chains 144 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN c 17 GLN c 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080806 restraints weight = 7454.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083153 restraints weight = 3517.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084660 restraints weight = 2120.191| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3458 Z= 0.206 Angle : 0.830 14.343 4711 Z= 0.413 Chirality : 0.049 0.158 547 Planarity : 0.005 0.040 612 Dihedral : 5.331 28.354 483 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer: Outliers : 5.65 % Allowed : 25.81 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.39), residues: 426 helix: -0.93 (0.83), residues: 44 sheet: -1.56 (0.41), residues: 156 loop : -2.59 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 113 PHE 0.029 0.002 PHE L 74 TYR 0.021 0.002 TYR H 35 ARG 0.003 0.001 ARG c 109 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 99) hydrogen bonds : angle 5.33341 ( 264) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.47577 ( 2) covalent geometry : bond 0.00474 ( 3457) covalent geometry : angle 0.82993 ( 4709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8773 (m) cc_final: 0.8479 (p) REVERT: H 41 ARG cc_start: 0.7542 (ptp-170) cc_final: 0.5821 (mmm160) REVERT: H 55 SER cc_start: 0.9172 (t) cc_final: 0.8904 (m) REVERT: H 75 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7878 (mmm160) REVERT: c 27 ASN cc_start: 0.8778 (t0) cc_final: 0.8274 (t0) REVERT: c 65 GLN cc_start: 0.7846 (pt0) cc_final: 0.7520 (tt0) REVERT: c 87 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7455 (mm-40) REVERT: c 103 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7795 (mm-30) REVERT: c 123 ASP cc_start: 0.7910 (t70) cc_final: 0.7458 (t0) REVERT: C 13 LYS cc_start: 0.9094 (tttp) cc_final: 0.8652 (ttpt) REVERT: C 123 ASP cc_start: 0.8776 (t70) cc_final: 0.7863 (t0) REVERT: C 127 GLN cc_start: 0.9405 (mp10) cc_final: 0.8929 (mp-120) REVERT: C 129 ASN cc_start: 0.8307 (m-40) cc_final: 0.7760 (m110) REVERT: L 13 SER cc_start: 0.7275 (m) cc_final: 0.6889 (p) REVERT: L 45 GLU cc_start: 0.8181 (pm20) cc_final: 0.7555 (pm20) REVERT: L 50 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8488 (mm) REVERT: L 93 GLN cc_start: 0.8953 (pm20) cc_final: 0.8670 (pm20) outliers start: 21 outliers final: 18 residues processed: 136 average time/residue: 0.1610 time to fit residues: 26.0740 Evaluate side-chains 145 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082673 restraints weight = 7294.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085130 restraints weight = 3416.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086712 restraints weight = 2046.449| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3458 Z= 0.153 Angle : 0.814 13.853 4711 Z= 0.404 Chirality : 0.049 0.175 547 Planarity : 0.005 0.041 612 Dihedral : 5.143 26.414 483 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 5.65 % Allowed : 26.08 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.38), residues: 426 helix: -0.92 (0.83), residues: 44 sheet: -1.54 (0.42), residues: 145 loop : -2.60 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 PHE 0.026 0.002 PHE L 74 TYR 0.019 0.001 TYR H 35 ARG 0.004 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 99) hydrogen bonds : angle 5.35415 ( 264) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.30822 ( 2) covalent geometry : bond 0.00350 ( 3457) covalent geometry : angle 0.81446 ( 4709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8784 (m) cc_final: 0.8498 (p) REVERT: H 41 ARG cc_start: 0.7616 (ptp-170) cc_final: 0.5934 (mmm160) REVERT: H 62 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6402 (p90) REVERT: H 75 ARG cc_start: 0.8296 (mmm160) cc_final: 0.8017 (mmm160) REVERT: c 27 ASN cc_start: 0.8723 (t0) cc_final: 0.8207 (t0) REVERT: c 46 LYS cc_start: 0.9311 (mttp) cc_final: 0.9104 (mttm) REVERT: c 65 GLN cc_start: 0.7724 (pt0) cc_final: 0.7463 (tt0) REVERT: c 87 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7456 (mm-40) REVERT: c 103 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7748 (mm-30) REVERT: c 122 ILE cc_start: 0.8862 (pp) cc_final: 0.8444 (mm) REVERT: c 123 ASP cc_start: 0.7889 (t70) cc_final: 0.7329 (t0) REVERT: C 13 LYS cc_start: 0.9036 (tttp) cc_final: 0.8651 (ttpt) REVERT: C 123 ASP cc_start: 0.8717 (t70) cc_final: 0.7784 (t0) REVERT: C 127 GLN cc_start: 0.9416 (mp10) cc_final: 0.8884 (mp-120) REVERT: C 129 ASN cc_start: 0.8660 (m-40) cc_final: 0.8098 (m110) REVERT: L 13 SER cc_start: 0.7278 (m) cc_final: 0.6928 (p) REVERT: L 50 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8347 (mm) REVERT: L 93 GLN cc_start: 0.8999 (pm20) cc_final: 0.8499 (pm20) outliers start: 21 outliers final: 16 residues processed: 141 average time/residue: 0.1584 time to fit residues: 26.5812 Evaluate side-chains 147 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 115 LEU Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084073 restraints weight = 7439.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086560 restraints weight = 3441.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088085 restraints weight = 2043.214| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3458 Z= 0.137 Angle : 0.852 15.266 4711 Z= 0.415 Chirality : 0.049 0.185 547 Planarity : 0.005 0.040 612 Dihedral : 5.006 26.251 483 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 4.30 % Allowed : 28.23 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.38), residues: 426 helix: -0.88 (0.82), residues: 44 sheet: -1.33 (0.43), residues: 145 loop : -2.51 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 PHE 0.032 0.002 PHE L 74 TYR 0.016 0.001 TYR H 35 ARG 0.005 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 99) hydrogen bonds : angle 5.28889 ( 264) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.27225 ( 2) covalent geometry : bond 0.00307 ( 3457) covalent geometry : angle 0.85172 ( 4709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 VAL cc_start: 0.8858 (m) cc_final: 0.8625 (p) REVERT: H 41 ARG cc_start: 0.7434 (ptp-170) cc_final: 0.5781 (mmm160) REVERT: H 62 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.6377 (p90) REVERT: H 75 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8027 (mmm160) REVERT: c 4 GLU cc_start: 0.8047 (tp30) cc_final: 0.7611 (tp30) REVERT: c 27 ASN cc_start: 0.8677 (t0) cc_final: 0.8152 (t0) REVERT: c 65 GLN cc_start: 0.7738 (pt0) cc_final: 0.7536 (tt0) REVERT: c 87 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7433 (mm-40) REVERT: c 103 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7763 (mm-30) REVERT: c 104 GLU cc_start: 0.8389 (pt0) cc_final: 0.7973 (pt0) REVERT: c 122 ILE cc_start: 0.8718 (pp) cc_final: 0.8462 (mm) REVERT: c 123 ASP cc_start: 0.7898 (t70) cc_final: 0.7317 (t0) REVERT: C 13 LYS cc_start: 0.8965 (tttp) cc_final: 0.8459 (ttpt) REVERT: C 123 ASP cc_start: 0.8707 (t70) cc_final: 0.7647 (t0) REVERT: C 127 GLN cc_start: 0.9410 (mp10) cc_final: 0.8856 (mp-120) REVERT: C 129 ASN cc_start: 0.8426 (m-40) cc_final: 0.7842 (m110) REVERT: L 13 SER cc_start: 0.7422 (m) cc_final: 0.7111 (p) REVERT: L 20 GLU cc_start: 0.8566 (mp0) cc_final: 0.8336 (pm20) REVERT: L 50 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8255 (mm) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.1686 time to fit residues: 28.9352 Evaluate side-chains 141 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.077973 restraints weight = 7568.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080335 restraints weight = 3552.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081815 restraints weight = 2145.215| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 3458 Z= 0.278 Angle : 0.902 15.053 4711 Z= 0.445 Chirality : 0.051 0.163 547 Planarity : 0.005 0.042 612 Dihedral : 5.392 23.419 483 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer: Outliers : 5.65 % Allowed : 26.88 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.39), residues: 426 helix: -1.25 (0.77), residues: 44 sheet: -1.49 (0.41), residues: 161 loop : -2.44 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 113 PHE 0.052 0.003 PHE L 74 TYR 0.022 0.002 TYR H 35 ARG 0.005 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 99) hydrogen bonds : angle 5.65285 ( 264) SS BOND : bond 0.00272 ( 1) SS BOND : angle 0.37450 ( 2) covalent geometry : bond 0.00639 ( 3457) covalent geometry : angle 0.90206 ( 4709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.60 seconds wall clock time: 25 minutes 1.18 seconds (1501.18 seconds total)