Starting phenix.real_space_refine on Sat Apr 26 21:23:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz4_37946/04_2025/8wz4_37946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz4_37946/04_2025/8wz4_37946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz4_37946/04_2025/8wz4_37946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz4_37946/04_2025/8wz4_37946.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz4_37946/04_2025/8wz4_37946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz4_37946/04_2025/8wz4_37946.cif" } resolution = 3.13 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= -0.001 sd= 0.014 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 16 5.16 5 C 2198 2.51 5 N 564 2.21 5 O 663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3441 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1685 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 925 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Time building chain proxies: 4.44, per 1000 atoms: 1.29 Number of scatterers: 3441 At special positions: 0 Unit cell: (88.692, 82.468, 70.798, 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 16 16.00 O 663 8.00 N 564 7.00 C 2198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.25 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 483.5 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 27.6% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 73 through 98 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 209 Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.758A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.004A pdb=" N THR H 91 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.343A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ARG C 49 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY C 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 301 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 300 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N MET C 289 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLN C 302 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER C 287 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.546A pdb=" N VAL H 18 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 78 " --> pdb=" O GLU H 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.638A pdb=" N THR H 113 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.638A pdb=" N THR H 113 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG H 98 " --> pdb=" O TYR H 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 46 154 hydrogen bonds defined for protein. 417 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: 0.86 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 564 1.28 - 1.41: 843 1.41 - 1.54: 2069 1.54 - 1.67: 5 1.67 - 1.81: 24 Bond restraints: 3505 Sorted by residual: bond pdb=" C VAL C 164 " pdb=" O VAL C 164 " ideal model delta sigma weight residual 1.237 1.145 0.092 1.19e-02 7.06e+03 5.99e+01 bond pdb=" N VAL C 164 " pdb=" CA VAL C 164 " ideal model delta sigma weight residual 1.460 1.369 0.091 1.21e-02 6.83e+03 5.65e+01 bond pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.30e-02 5.92e+03 4.82e+01 bond pdb=" N LYS C 166 " pdb=" CA LYS C 166 " ideal model delta sigma weight residual 1.459 1.380 0.079 1.20e-02 6.94e+03 4.35e+01 bond pdb=" C ALA C 170 " pdb=" N LEU C 171 " ideal model delta sigma weight residual 1.331 1.416 -0.084 1.32e-02 5.74e+03 4.09e+01 ... (remaining 3500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 4645 2.53 - 5.05: 84 5.05 - 7.58: 10 7.58 - 10.10: 7 10.10 - 12.63: 1 Bond angle restraints: 4747 Sorted by residual: angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 110.72 103.29 7.43 1.01e+00 9.80e-01 5.41e+01 angle pdb=" N GLU C 163 " pdb=" CA GLU C 163 " pdb=" C GLU C 163 " ideal model delta sigma weight residual 111.28 119.14 -7.86 1.09e+00 8.42e-01 5.19e+01 angle pdb=" CA LYS C 166 " pdb=" C LYS C 166 " pdb=" N ILE C 167 " ideal model delta sigma weight residual 117.17 124.76 -7.59 1.18e+00 7.18e-01 4.14e+01 angle pdb=" N LEU C 171 " pdb=" CA LEU C 171 " pdb=" C LEU C 171 " ideal model delta sigma weight residual 112.72 105.07 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" CA VAL C 164 " pdb=" C VAL C 164 " pdb=" N ASN C 165 " ideal model delta sigma weight residual 117.28 123.60 -6.32 1.16e+00 7.43e-01 2.97e+01 ... (remaining 4742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.95: 1806 13.95 - 27.91: 222 27.91 - 41.86: 57 41.86 - 55.81: 19 55.81 - 69.77: 5 Dihedral angle restraints: 2109 sinusoidal: 835 harmonic: 1274 Sorted by residual: dihedral pdb=" CB CYS C 155 " pdb=" SG CYS C 155 " pdb=" SG CYS C 290 " pdb=" CB CYS C 290 " ideal model delta sinusoidal sigma weight residual -86.00 -155.77 69.77 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -121.03 35.03 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CA ILE C 291 " pdb=" C ILE C 291 " pdb=" N ILE C 292 " pdb=" CA ILE C 292 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 2106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 529 0.120 - 0.240: 17 0.240 - 0.359: 2 0.359 - 0.479: 1 0.479 - 0.599: 1 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA GLU C 163 " pdb=" N GLU C 163 " pdb=" C GLU C 163 " pdb=" CB GLU C 163 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA LYS C 166 " pdb=" N LYS C 166 " pdb=" C LYS C 166 " pdb=" CB LYS C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 547 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 170 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ALA C 170 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA C 170 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU C 171 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 168 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS C 168 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C 168 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 169 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 167 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C ILE C 167 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE C 167 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C 168 " -0.016 2.00e-02 2.50e+03 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 84 2.67 - 3.23: 3256 3.23 - 3.79: 5006 3.79 - 4.34: 6907 4.34 - 4.90: 12143 Nonbonded interactions: 27396 Sorted by model distance: nonbonded pdb=" OH TYR H 99 " pdb=" OH TYR L 96 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR L 49 " pdb=" OD1 ASP L 56 " model vdw 2.302 3.040 nonbonded pdb=" O LEU C 252 " pdb=" NH1 ARG C 282 " model vdw 2.363 3.120 nonbonded pdb=" O THR H 110 " pdb=" OG1 THR H 110 " model vdw 2.369 3.040 ... (remaining 27391 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: 6.270 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.011 0.216 3509 Z= 0.630 Angle : 0.947 17.640 4755 Z= 0.559 Chirality : 0.062 0.599 550 Planarity : 0.005 0.042 593 Dihedral : 13.979 69.590 1279 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.26 % Allowed : 9.28 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -4.05 (0.33), residues: 431 helix: -1.06 (0.42), residues: 116 sheet: -2.97 (0.36), residues: 141 loop : -3.46 (0.35), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.004 0.002 HIS L 90 PHE 0.016 0.002 PHE L 91 TYR 0.018 0.002 TYR H 80 ARG 0.003 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.18201 ( 150) hydrogen bonds : angle 7.47988 ( 417) SS BOND : bond 0.10782 ( 4) SS BOND : angle 7.62357 ( 8) covalent geometry : bond 0.00998 ( 3505) covalent geometry : angle 0.89476 ( 4747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.414 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1642 time to fit residues: 22.4409 Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN L 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126087 restraints weight = 4608.712| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.14 r_work: 0.3420 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3509 Z= 0.138 Angle : 0.591 7.836 4755 Z= 0.312 Chirality : 0.044 0.207 550 Planarity : 0.004 0.033 593 Dihedral : 5.313 48.479 466 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.32 % Allowed : 14.43 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -2.31 (0.38), residues: 431 helix: 1.02 (0.49), residues: 116 sheet: -2.36 (0.38), residues: 139 loop : -2.52 (0.40), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS C 159 PHE 0.019 0.002 PHE H 70 TYR 0.012 0.002 TYR H 80 ARG 0.007 0.001 ARG C 282 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 150) hydrogen bonds : angle 5.01570 ( 417) SS BOND : bond 0.00547 ( 4) SS BOND : angle 0.94751 ( 8) covalent geometry : bond 0.00320 ( 3505) covalent geometry : angle 0.58977 ( 4747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.384 Fit side-chains REVERT: C 77 LYS cc_start: 0.7704 (tptm) cc_final: 0.7183 (ttpt) REVERT: L 31 ASN cc_start: 0.7874 (t0) cc_final: 0.7646 (t0) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.1764 time to fit residues: 16.1617 Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.149542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124866 restraints weight = 4611.278| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.18 r_work: 0.3397 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3509 Z= 0.137 Angle : 0.570 7.699 4755 Z= 0.299 Chirality : 0.043 0.167 550 Planarity : 0.003 0.030 593 Dihedral : 5.081 40.192 466 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.09 % Allowed : 17.27 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.35 (0.40), residues: 431 helix: 1.90 (0.49), residues: 116 sheet: -1.71 (0.39), residues: 144 loop : -2.08 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS C 159 PHE 0.011 0.001 PHE H 70 TYR 0.011 0.002 TYR C 299 ARG 0.003 0.001 ARG C 282 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 150) hydrogen bonds : angle 4.65107 ( 417) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.12532 ( 8) covalent geometry : bond 0.00322 ( 3505) covalent geometry : angle 0.56898 ( 4747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.363 Fit side-chains REVERT: C 77 LYS cc_start: 0.7665 (tptm) cc_final: 0.7305 (ttpt) REVERT: C 80 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7392 (mtmt) REVERT: C 222 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7390 (mt-10) REVERT: C 289 MET cc_start: 0.9200 (tpt) cc_final: 0.8518 (tpt) REVERT: H 32 TYR cc_start: 0.8779 (m-80) cc_final: 0.8511 (m-80) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.1687 time to fit residues: 17.0809 Evaluate side-chains 74 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120601 restraints weight = 4747.100| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.25 r_work: 0.3337 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3509 Z= 0.198 Angle : 0.625 8.040 4755 Z= 0.328 Chirality : 0.044 0.155 550 Planarity : 0.003 0.024 593 Dihedral : 5.321 37.266 466 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.90 % Allowed : 17.53 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.18 (0.41), residues: 431 helix: 1.85 (0.49), residues: 116 sheet: -1.48 (0.38), residues: 159 loop : -1.95 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 52 HIS 0.004 0.002 HIS L 90 PHE 0.013 0.002 PHE L 91 TYR 0.018 0.002 TYR C 86 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 150) hydrogen bonds : angle 4.85196 ( 417) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.45023 ( 8) covalent geometry : bond 0.00472 ( 3505) covalent geometry : angle 0.62282 ( 4747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7571 (tptm) cc_final: 0.7252 (ttpt) REVERT: C 80 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7683 (mttt) REVERT: C 222 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7512 (mt-10) REVERT: C 263 ASP cc_start: 0.8125 (t0) cc_final: 0.7703 (m-30) REVERT: C 289 MET cc_start: 0.9211 (tpt) cc_final: 0.8606 (tpt) REVERT: H 73 GLU cc_start: 0.7221 (mp0) cc_final: 0.6497 (mp0) REVERT: L 18 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8077 (m) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.1702 time to fit residues: 16.7325 Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.144359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119650 restraints weight = 4799.323| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.20 r_work: 0.3346 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3509 Z= 0.185 Angle : 0.600 7.727 4755 Z= 0.313 Chirality : 0.043 0.183 550 Planarity : 0.003 0.024 593 Dihedral : 5.136 33.368 466 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.38 % Allowed : 20.10 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.00 (0.41), residues: 431 helix: 2.04 (0.50), residues: 116 sheet: -1.25 (0.39), residues: 156 loop : -2.04 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 PHE 0.012 0.002 PHE L 91 TYR 0.020 0.002 TYR C 86 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 150) hydrogen bonds : angle 4.69659 ( 417) SS BOND : bond 0.00355 ( 4) SS BOND : angle 1.22177 ( 8) covalent geometry : bond 0.00445 ( 3505) covalent geometry : angle 0.59873 ( 4747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7505 (tptm) cc_final: 0.7212 (ttpt) REVERT: C 80 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7649 (mttt) REVERT: C 222 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 263 ASP cc_start: 0.8233 (t0) cc_final: 0.7680 (m-30) REVERT: C 289 MET cc_start: 0.9259 (tpt) cc_final: 0.8499 (tpt) REVERT: H 73 GLU cc_start: 0.7189 (mp0) cc_final: 0.6463 (mp0) REVERT: L 18 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (m) outliers start: 17 outliers final: 12 residues processed: 80 average time/residue: 0.1644 time to fit residues: 16.2801 Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118244 restraints weight = 4913.534| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.25 r_work: 0.3309 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3509 Z= 0.184 Angle : 0.593 7.575 4755 Z= 0.312 Chirality : 0.043 0.156 550 Planarity : 0.003 0.025 593 Dihedral : 5.073 28.802 466 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.67 % Allowed : 19.85 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.88 (0.41), residues: 431 helix: 2.06 (0.50), residues: 116 sheet: -1.14 (0.40), residues: 156 loop : -1.96 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.012 0.002 PHE L 91 TYR 0.019 0.002 TYR C 86 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 150) hydrogen bonds : angle 4.69338 ( 417) SS BOND : bond 0.00367 ( 4) SS BOND : angle 1.18456 ( 8) covalent geometry : bond 0.00442 ( 3505) covalent geometry : angle 0.59143 ( 4747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7464 (tptm) cc_final: 0.7230 (ttpt) REVERT: C 80 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7683 (mttt) REVERT: C 222 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 263 ASP cc_start: 0.8213 (t0) cc_final: 0.7610 (m-30) REVERT: C 289 MET cc_start: 0.9277 (tpt) cc_final: 0.8446 (tpt) REVERT: H 32 TYR cc_start: 0.8753 (m-80) cc_final: 0.8319 (m-80) REVERT: H 73 GLU cc_start: 0.7195 (mp0) cc_final: 0.6412 (mp0) REVERT: L 18 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8080 (m) REVERT: L 81 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7829 (pm20) outliers start: 22 outliers final: 18 residues processed: 80 average time/residue: 0.1515 time to fit residues: 15.0422 Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.142724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117958 restraints weight = 4781.683| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.23 r_work: 0.3303 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3509 Z= 0.183 Angle : 0.579 7.397 4755 Z= 0.305 Chirality : 0.043 0.152 550 Planarity : 0.003 0.025 593 Dihedral : 5.006 24.366 466 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 6.19 % Allowed : 20.88 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.84 (0.41), residues: 431 helix: 2.04 (0.49), residues: 116 sheet: -1.09 (0.40), residues: 157 loop : -1.91 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.012 0.002 PHE L 91 TYR 0.021 0.002 TYR C 86 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 150) hydrogen bonds : angle 4.70132 ( 417) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.18431 ( 8) covalent geometry : bond 0.00441 ( 3505) covalent geometry : angle 0.57729 ( 4747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.387 Fit side-chains REVERT: C 77 LYS cc_start: 0.7410 (tptm) cc_final: 0.7182 (ttpt) REVERT: C 222 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7605 (mt-10) REVERT: C 263 ASP cc_start: 0.8214 (t0) cc_final: 0.7598 (m-30) REVERT: C 289 MET cc_start: 0.9296 (tpt) cc_final: 0.8418 (tpt) REVERT: H 32 TYR cc_start: 0.8752 (m-80) cc_final: 0.8336 (m-80) REVERT: L 18 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8050 (m) REVERT: L 81 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8026 (pt0) outliers start: 24 outliers final: 19 residues processed: 78 average time/residue: 0.1456 time to fit residues: 14.2269 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.148654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124550 restraints weight = 4787.261| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.14 r_work: 0.3391 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3509 Z= 0.159 Angle : 0.554 7.037 4755 Z= 0.293 Chirality : 0.042 0.154 550 Planarity : 0.003 0.027 593 Dihedral : 4.856 23.682 466 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.67 % Allowed : 21.65 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.73 (0.42), residues: 431 helix: 2.39 (0.50), residues: 110 sheet: -0.96 (0.41), residues: 153 loop : -1.97 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.011 0.001 PHE L 91 TYR 0.018 0.002 TYR C 86 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 150) hydrogen bonds : angle 4.58190 ( 417) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.08742 ( 8) covalent geometry : bond 0.00383 ( 3505) covalent geometry : angle 0.55292 ( 4747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.371 Fit side-chains REVERT: C 222 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7599 (mt-10) REVERT: C 263 ASP cc_start: 0.8227 (t0) cc_final: 0.7644 (m-30) REVERT: C 289 MET cc_start: 0.9295 (tpt) cc_final: 0.8380 (tpt) REVERT: H 32 TYR cc_start: 0.8751 (m-80) cc_final: 0.8332 (m-80) REVERT: L 18 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8080 (m) REVERT: L 81 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8043 (pt0) outliers start: 22 outliers final: 19 residues processed: 73 average time/residue: 0.1429 time to fit residues: 13.1670 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.141068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117853 restraints weight = 4660.583| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.07 r_work: 0.3293 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3509 Z= 0.138 Angle : 0.540 6.641 4755 Z= 0.286 Chirality : 0.041 0.154 550 Planarity : 0.003 0.027 593 Dihedral : 4.651 23.180 466 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.15 % Allowed : 21.65 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.58 (0.42), residues: 431 helix: 2.52 (0.50), residues: 110 sheet: -0.83 (0.42), residues: 153 loop : -1.93 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.009 0.001 PHE L 91 TYR 0.016 0.002 TYR C 86 ARG 0.001 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 150) hydrogen bonds : angle 4.44115 ( 417) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.97441 ( 8) covalent geometry : bond 0.00330 ( 3505) covalent geometry : angle 0.53897 ( 4747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.405 Fit side-chains REVERT: C 263 ASP cc_start: 0.8152 (t0) cc_final: 0.7532 (m-30) REVERT: C 289 MET cc_start: 0.9259 (tpt) cc_final: 0.8327 (tpt) REVERT: H 32 TYR cc_start: 0.8706 (m-80) cc_final: 0.8308 (m-80) outliers start: 20 outliers final: 18 residues processed: 78 average time/residue: 0.1416 time to fit residues: 13.9196 Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116665 restraints weight = 4753.160| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.09 r_work: 0.3292 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3509 Z= 0.161 Angle : 0.567 6.930 4755 Z= 0.300 Chirality : 0.042 0.154 550 Planarity : 0.004 0.028 593 Dihedral : 4.740 23.626 466 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.64 % Allowed : 22.16 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.59 (0.42), residues: 431 helix: 2.43 (0.50), residues: 110 sheet: -0.83 (0.42), residues: 155 loop : -1.88 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.011 0.001 PHE L 91 TYR 0.017 0.002 TYR C 86 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 150) hydrogen bonds : angle 4.54070 ( 417) SS BOND : bond 0.00295 ( 4) SS BOND : angle 1.15833 ( 8) covalent geometry : bond 0.00386 ( 3505) covalent geometry : angle 0.56501 ( 4747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.406 Fit side-chains REVERT: C 263 ASP cc_start: 0.8169 (t0) cc_final: 0.7549 (m-30) REVERT: C 289 MET cc_start: 0.9271 (tpt) cc_final: 0.8391 (tpt) REVERT: H 32 TYR cc_start: 0.8717 (m-80) cc_final: 0.8285 (m-80) outliers start: 18 outliers final: 17 residues processed: 70 average time/residue: 0.1339 time to fit residues: 11.9642 Evaluate side-chains 74 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.140771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117560 restraints weight = 4795.667| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.11 r_work: 0.3305 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3509 Z= 0.138 Angle : 0.541 6.648 4755 Z= 0.286 Chirality : 0.041 0.153 550 Planarity : 0.003 0.027 593 Dihedral : 4.627 23.229 466 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.38 % Allowed : 22.94 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.49 (0.42), residues: 431 helix: 2.47 (0.50), residues: 110 sheet: -0.65 (0.43), residues: 153 loop : -1.92 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.009 0.001 PHE H 70 TYR 0.016 0.002 TYR C 86 ARG 0.001 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 150) hydrogen bonds : angle 4.47313 ( 417) SS BOND : bond 0.00273 ( 4) SS BOND : angle 1.05613 ( 8) covalent geometry : bond 0.00332 ( 3505) covalent geometry : angle 0.53978 ( 4747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.73 seconds wall clock time: 44 minutes 54.73 seconds (2694.73 seconds total)