Starting phenix.real_space_refine on Wed Jul 23 16:55:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v24_31636/07_2025/7v24_31636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v24_31636/07_2025/7v24_31636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v24_31636/07_2025/7v24_31636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v24_31636/07_2025/7v24_31636.map" model { file = "/net/cci-nas-00/data/ceres_data/7v24_31636/07_2025/7v24_31636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v24_31636/07_2025/7v24_31636.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 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 14 5.16 5 C 2436 2.51 5 N 636 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3814 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2096 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Time building chain proxies: 3.63, per 1000 atoms: 0.95 Number of scatterers: 3814 At special positions: 0 Unit cell: (77.76, 76.68, 98.28, 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 14 16.00 O 728 8.00 N 636 7.00 C 2436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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: 0.94 Conformation dependent library (CDL) restraints added in 425.1 milliseconds 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 894 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 6.8% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 26 through 32 removed outlier: 3.598A pdb=" N PHE H 29 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.558A pdb=" N TYR H 110 " --> pdb=" O TRP H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.721A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.568A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.528A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.528A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.711A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.995A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.883A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 154 through 160 removed outlier: 9.883A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 336 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: 1.11 Time building geometry restraints manager: 1.03 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: 1209 1.34 - 1.47: 1061 1.47 - 1.59: 1626 1.59 - 1.71: 0 1.71 - 1.83: 19 Bond restraints: 3915 Sorted by residual: bond pdb=" CA SER A 151 " pdb=" CB SER A 151 " ideal model delta sigma weight residual 1.532 1.473 0.059 2.23e-02 2.01e+03 7.10e+00 bond pdb=" N SER A 151 " pdb=" CA SER A 151 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.00e-02 1.00e+04 5.83e+00 bond pdb=" N TRP A 152 " pdb=" CA TRP A 152 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.24e-02 6.50e+03 4.34e+00 bond pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.58e+00 bond pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta sigma weight residual 1.463 1.486 -0.023 1.27e-02 6.20e+03 3.33e+00 ... (remaining 3910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 5176 2.11 - 4.22: 131 4.22 - 6.32: 15 6.32 - 8.43: 1 8.43 - 10.54: 2 Bond angle restraints: 5325 Sorted by residual: angle pdb=" C ARG A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N ALA A 123 " pdb=" CA ALA A 123 " pdb=" C ALA A 123 " ideal model delta sigma weight residual 114.62 110.69 3.93 1.14e+00 7.69e-01 1.19e+01 angle pdb=" CA TRP A 152 " pdb=" C TRP A 152 " pdb=" O TRP A 152 " ideal model delta sigma weight residual 120.55 117.08 3.47 1.07e+00 8.73e-01 1.05e+01 angle pdb=" N SER A 151 " pdb=" CA SER A 151 " pdb=" C SER A 151 " ideal model delta sigma weight residual 112.54 107.75 4.79 1.51e+00 4.39e-01 1.01e+01 angle pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 119.71 116.08 3.63 1.17e+00 7.31e-01 9.63e+00 ... (remaining 5320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2052 17.09 - 34.18: 195 34.18 - 51.27: 25 51.27 - 68.36: 4 68.36 - 85.45: 6 Dihedral angle restraints: 2282 sinusoidal: 878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA PHE A 79 " pdb=" C PHE A 79 " pdb=" N ASP A 80 " pdb=" CA ASP A 80 " ideal model delta harmonic sigma weight residual 180.00 148.24 31.76 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 49.29 43.71 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CA THR A 95 " pdb=" C THR A 95 " pdb=" N GLU A 96 " pdb=" CA GLU A 96 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 2279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 423 0.048 - 0.095: 119 0.095 - 0.143: 33 0.143 - 0.191: 3 0.191 - 0.238: 2 Chirality restraints: 580 Sorted by residual: chirality pdb=" CG LEU A 216 " pdb=" CB LEU A 216 " pdb=" CD1 LEU A 216 " pdb=" CD2 LEU A 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR A 33 " pdb=" CA THR A 33 " pdb=" OG1 THR A 33 " pdb=" CG2 THR A 33 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASP A 80 " pdb=" N ASP A 80 " pdb=" C ASP A 80 " pdb=" CB ASP A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 577 not shown) Planarity restraints: 682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO L 8 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 266 " -0.011 2.00e-02 2.50e+03 1.61e-02 5.19e+00 pdb=" CG TYR A 266 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 266 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 266 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 266 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 266 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 266 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 266 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 250 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 251 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.023 5.00e-02 4.00e+02 ... (remaining 679 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 197 2.71 - 3.26: 3714 3.26 - 3.81: 6069 3.81 - 4.35: 7911 4.35 - 4.90: 13988 Nonbonded interactions: 31879 Sorted by model distance: nonbonded pdb=" OH TYR H 110 " pdb=" OH TYR A 144 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU A 156 " model vdw 2.166 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.174 3.040 nonbonded pdb=" OG SER H 33 " pdb=" O GLY H 101 " model vdw 2.175 3.040 nonbonded pdb=" NE2 GLN H 39 " pdb=" O LYS H 43 " model vdw 2.196 3.120 ... (remaining 31874 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: 7.500 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.030 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 3919 Z= 0.275 Angle : 0.799 10.541 5333 Z= 0.452 Chirality : 0.049 0.238 580 Planarity : 0.005 0.058 682 Dihedral : 13.640 85.447 1376 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.37), residues: 479 helix: -4.96 (0.48), residues: 6 sheet: -0.76 (0.40), residues: 164 loop : -1.47 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.003 0.001 HIS A 66 PHE 0.015 0.002 PHE A 86 TYR 0.038 0.002 TYR A 266 ARG 0.005 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.23326 ( 131) hydrogen bonds : angle 10.15741 ( 336) SS BOND : bond 0.00345 ( 4) SS BOND : angle 1.44644 ( 8) covalent geometry : bond 0.00612 ( 3915) covalent geometry : angle 0.79812 ( 5325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.1915 time to fit residues: 19.6075 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097560 restraints weight = 5289.956| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.18 r_work: 0.2933 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3919 Z= 0.193 Angle : 0.706 8.374 5333 Z= 0.366 Chirality : 0.047 0.184 580 Planarity : 0.005 0.051 682 Dihedral : 6.379 54.171 531 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.95 % Allowed : 8.10 % Favored : 90.95 % 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: -1.64 (0.38), residues: 479 helix: -5.17 (0.33), residues: 6 sheet: -0.51 (0.41), residues: 160 loop : -1.37 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS A 207 PHE 0.014 0.002 PHE H 29 TYR 0.027 0.002 TYR A 266 ARG 0.003 0.001 ARG A 34 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 131) hydrogen bonds : angle 7.07673 ( 336) SS BOND : bond 0.00595 ( 4) SS BOND : angle 1.23849 ( 8) covalent geometry : bond 0.00454 ( 3915) covalent geometry : angle 0.70524 ( 5325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 57 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7296 (mm-40) REVERT: H 82 GLN cc_start: 0.8244 (mm-40) cc_final: 0.8018 (mm-40) REVERT: A 41 LYS cc_start: 0.5831 (tptt) cc_final: 0.5184 (tptt) outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.2190 time to fit residues: 18.8478 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain A residue 276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098623 restraints weight = 5231.995| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.14 r_work: 0.2899 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 3919 Z= 0.234 Angle : 0.703 7.259 5333 Z= 0.363 Chirality : 0.048 0.180 580 Planarity : 0.005 0.048 682 Dihedral : 5.693 28.351 529 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.38 % Allowed : 11.67 % Favored : 85.95 % 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: -1.40 (0.39), residues: 479 helix: -5.17 (0.33), residues: 6 sheet: -0.35 (0.38), residues: 182 loop : -1.23 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 66 PHE 0.015 0.002 PHE H 29 TYR 0.022 0.002 TYR A 266 ARG 0.002 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 131) hydrogen bonds : angle 6.51268 ( 336) SS BOND : bond 0.00412 ( 4) SS BOND : angle 1.28497 ( 8) covalent geometry : bond 0.00559 ( 3915) covalent geometry : angle 0.70151 ( 5325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.444 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.1657 time to fit residues: 14.4412 Evaluate side-chains 59 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095032 restraints weight = 5368.817| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.25 r_work: 0.2926 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3919 Z= 0.186 Angle : 0.654 7.205 5333 Z= 0.339 Chirality : 0.045 0.176 580 Planarity : 0.004 0.045 682 Dihedral : 5.473 28.313 529 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 3.10 % Allowed : 11.19 % Favored : 85.71 % 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: -1.42 (0.38), residues: 479 helix: -5.15 (0.34), residues: 6 sheet: -0.36 (0.40), residues: 170 loop : -1.23 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.014 0.002 PHE H 29 TYR 0.017 0.002 TYR A 266 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 131) hydrogen bonds : angle 6.09884 ( 336) SS BOND : bond 0.00401 ( 4) SS BOND : angle 1.16500 ( 8) covalent geometry : bond 0.00436 ( 3915) covalent geometry : angle 0.65252 ( 5325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.454 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.2257 time to fit residues: 19.7368 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 153 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.097952 restraints weight = 5384.090| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.20 r_work: 0.2950 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3919 Z= 0.141 Angle : 0.614 7.314 5333 Z= 0.319 Chirality : 0.044 0.172 580 Planarity : 0.004 0.042 682 Dihedral : 5.242 28.164 529 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 3.10 % Allowed : 12.86 % Favored : 84.05 % 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: -1.24 (0.39), residues: 479 helix: -5.14 (0.35), residues: 6 sheet: -0.28 (0.39), residues: 179 loop : -1.08 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.015 0.001 TYR A 266 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 131) hydrogen bonds : angle 5.83824 ( 336) SS BOND : bond 0.00393 ( 4) SS BOND : angle 1.04587 ( 8) covalent geometry : bond 0.00328 ( 3915) covalent geometry : angle 0.61267 ( 5325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 66 average time/residue: 0.1720 time to fit residues: 14.5338 Evaluate side-chains 61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102539 restraints weight = 5150.617| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.11 r_work: 0.2914 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3919 Z= 0.220 Angle : 0.656 7.534 5333 Z= 0.339 Chirality : 0.045 0.172 580 Planarity : 0.004 0.042 682 Dihedral : 5.355 28.125 529 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.62 % Allowed : 15.71 % Favored : 81.67 % 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: -1.24 (0.39), residues: 479 helix: -5.15 (0.34), residues: 6 sheet: -0.28 (0.39), residues: 179 loop : -1.08 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.002 PHE H 29 TYR 0.015 0.002 TYR A 266 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 131) hydrogen bonds : angle 5.85441 ( 336) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.50042 ( 8) covalent geometry : bond 0.00529 ( 3915) covalent geometry : angle 0.65389 ( 5325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.424 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.1761 time to fit residues: 15.0856 Evaluate side-chains 62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.0060 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097511 restraints weight = 5336.475| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.25 r_work: 0.2952 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3919 Z= 0.123 Angle : 0.590 7.295 5333 Z= 0.307 Chirality : 0.043 0.167 580 Planarity : 0.004 0.041 682 Dihedral : 5.076 27.666 529 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.95 % 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: -1.20 (0.39), residues: 479 helix: -5.14 (0.35), residues: 6 sheet: -0.24 (0.40), residues: 171 loop : -1.05 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.012 0.001 PHE H 29 TYR 0.012 0.001 TYR H 32 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 131) hydrogen bonds : angle 5.55816 ( 336) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.98134 ( 8) covalent geometry : bond 0.00283 ( 3915) covalent geometry : angle 0.58962 ( 5325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7994 (mppt) cc_final: 0.7723 (mmtm) REVERT: A 53 ASP cc_start: 0.8550 (t70) cc_final: 0.8126 (t70) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.1701 time to fit residues: 15.0326 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101799 restraints weight = 5158.674| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.14 r_work: 0.2917 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3919 Z= 0.192 Angle : 0.627 7.877 5333 Z= 0.325 Chirality : 0.044 0.168 580 Planarity : 0.004 0.040 682 Dihedral : 5.166 28.048 529 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 2.62 % Allowed : 18.33 % Favored : 79.05 % 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: -1.02 (0.39), residues: 479 helix: None (None), residues: 0 sheet: -0.19 (0.39), residues: 179 loop : -0.99 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.012 0.001 PHE H 29 TYR 0.014 0.002 TYR H 95 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 131) hydrogen bonds : angle 5.58178 ( 336) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.17181 ( 8) covalent geometry : bond 0.00459 ( 3915) covalent geometry : angle 0.62595 ( 5325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8540 (t70) cc_final: 0.8150 (t70) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.2991 time to fit residues: 23.6917 Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099331 restraints weight = 5245.042| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.18 r_work: 0.2910 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3919 Z= 0.189 Angle : 0.635 8.377 5333 Z= 0.327 Chirality : 0.044 0.165 580 Planarity : 0.004 0.040 682 Dihedral : 5.203 27.989 529 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 3.10 % Allowed : 17.62 % Favored : 79.29 % 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: -1.04 (0.39), residues: 479 helix: None (None), residues: 0 sheet: -0.18 (0.38), residues: 181 loop : -1.03 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.015 0.002 TYR H 95 ARG 0.002 0.000 ARG L 60 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 131) hydrogen bonds : angle 5.58866 ( 336) SS BOND : bond 0.00312 ( 4) SS BOND : angle 1.13527 ( 8) covalent geometry : bond 0.00449 ( 3915) covalent geometry : angle 0.63392 ( 5325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: L 60 ARG cc_start: 0.8545 (ptt90) cc_final: 0.8331 (ptt90) REVERT: A 53 ASP cc_start: 0.8530 (t70) cc_final: 0.8137 (t70) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.1405 time to fit residues: 11.1850 Evaluate side-chains 62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.093891 restraints weight = 5394.343| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.30 r_work: 0.2891 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3919 Z= 0.171 Angle : 0.626 8.495 5333 Z= 0.322 Chirality : 0.044 0.165 580 Planarity : 0.004 0.039 682 Dihedral : 5.174 27.945 529 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 2.62 % Allowed : 18.33 % Favored : 79.05 % 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: -0.96 (0.39), residues: 479 helix: None (None), residues: 0 sheet: -0.11 (0.39), residues: 179 loop : -0.98 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.012 0.001 PHE H 29 TYR 0.014 0.002 TYR H 95 ARG 0.003 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 131) hydrogen bonds : angle 5.51810 ( 336) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.06046 ( 8) covalent geometry : bond 0.00404 ( 3915) covalent geometry : angle 0.62516 ( 5325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8011 (mppt) cc_final: 0.7754 (mmtm) REVERT: L 60 ARG cc_start: 0.8504 (ptt90) cc_final: 0.8225 (ptt90) REVERT: A 53 ASP cc_start: 0.8484 (t70) cc_final: 0.8057 (t70) outliers start: 11 outliers final: 11 residues processed: 59 average time/residue: 0.1338 time to fit residues: 10.3422 Evaluate side-chains 59 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098056 restraints weight = 5225.078| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.15 r_work: 0.2897 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3919 Z= 0.207 Angle : 0.647 8.671 5333 Z= 0.333 Chirality : 0.045 0.166 580 Planarity : 0.004 0.040 682 Dihedral : 5.274 28.132 529 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.10 % Allowed : 17.86 % Favored : 79.05 % 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: -0.98 (0.39), residues: 479 helix: None (None), residues: 0 sheet: -0.12 (0.38), residues: 181 loop : -0.99 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE H 29 TYR 0.015 0.002 TYR H 95 ARG 0.002 0.000 ARG L 60 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 131) hydrogen bonds : angle 5.59229 ( 336) SS BOND : bond 0.00312 ( 4) SS BOND : angle 1.16588 ( 8) covalent geometry : bond 0.00495 ( 3915) covalent geometry : angle 0.64607 ( 5325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.44 seconds wall clock time: 57 minutes 36.37 seconds (3456.37 seconds total)