Starting phenix.real_space_refine on Mon Jan 13 17:52:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz4_37946/01_2025/8wz4_37946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz4_37946/01_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_37946/01_2025/8wz4_37946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz4_37946/01_2025/8wz4_37946.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz4_37946/01_2025/8wz4_37946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz4_37946/01_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-5571/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: 3.49, per 1000 atoms: 1.01 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: 0.82 Conformation dependent library (CDL) restraints added in 439.1 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: 0.42 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: 0.96 Time building geometry restraints manager: 0.96 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: 2.680 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: 13.630 Find NCS groups from input model: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- 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 : 0.010 0.092 3505 Z= 0.638 Angle : 0.895 12.627 4747 Z= 0.540 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 *********************** 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 : 0.385 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1621 time to fit residues: 22.2147 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 : 0.395 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125987 restraints weight = 4608.718| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.16 r_work: 0.3419 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 3505 Z= 0.205 Angle : 0.590 7.836 4747 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 *********************** 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 : 0.379 Fit side-chains REVERT: C 77 LYS cc_start: 0.7712 (tptm) cc_final: 0.7193 (ttpt) REVERT: L 31 ASN cc_start: 0.7876 (t0) cc_final: 0.7646 (t0) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.1800 time to fit residues: 16.5230 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 : 0.421 ------------------------------------------------------------------------------- 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: 0.5980 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.149220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124574 restraints weight = 4620.928| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.18 r_work: 0.3392 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3505 Z= 0.215 Angle : 0.576 7.691 4747 Z= 0.302 Chirality : 0.043 0.165 550 Planarity : 0.003 0.030 593 Dihedral : 5.116 41.410 466 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -1.41 (0.40), residues: 431 helix: 1.85 (0.49), residues: 116 sheet: -1.75 (0.39), residues: 144 loop : -2.12 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS C 159 PHE 0.013 0.001 PHE H 70 TYR 0.012 0.002 TYR H 80 ARG 0.003 0.001 ARG C 282 *********************** 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 87 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.478 Fit side-chains REVERT: C 77 LYS cc_start: 0.7687 (tptm) cc_final: 0.7228 (ttpt) REVERT: C 80 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7411 (mtmt) REVERT: C 289 MET cc_start: 0.9162 (tpt) cc_final: 0.8591 (tpt) REVERT: H 32 TYR cc_start: 0.8771 (m-80) cc_final: 0.8377 (m-80) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.1488 time to fit residues: 15.2555 Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.145153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119959 restraints weight = 4726.994| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.21 r_work: 0.3333 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3505 Z= 0.318 Angle : 0.628 8.040 4747 Z= 0.328 Chirality : 0.044 0.154 550 Planarity : 0.003 0.026 593 Dihedral : 5.402 39.125 466 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.90 % Allowed : 17.27 % Favored : 77.84 % 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: -1.24 (0.41), residues: 431 helix: 1.86 (0.49), residues: 116 sheet: -1.55 (0.38), residues: 159 loop : -2.00 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.004 0.002 HIS L 90 PHE 0.013 0.002 PHE L 91 TYR 0.013 0.002 TYR C 299 ARG 0.003 0.001 ARG C 282 *********************** 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 82 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7565 (tptm) cc_final: 0.7208 (ttpt) REVERT: C 80 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7642 (mttt) REVERT: C 222 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7714 (mt-10) REVERT: C 289 MET cc_start: 0.9224 (tpt) cc_final: 0.8617 (tpt) REVERT: H 63 ASP cc_start: 0.7952 (t0) cc_final: 0.7718 (t0) REVERT: L 18 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8073 (m) outliers start: 19 outliers final: 14 residues processed: 76 average time/residue: 0.1591 time to fit residues: 14.8595 Evaluate side-chains 76 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 0.0010 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.0070 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.148731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123959 restraints weight = 4739.749| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.21 r_work: 0.3380 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3505 Z= 0.179 Angle : 0.540 6.890 4747 Z= 0.281 Chirality : 0.041 0.156 550 Planarity : 0.003 0.027 593 Dihedral : 4.855 32.234 466 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.87 % Allowed : 19.59 % Favored : 76.55 % 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: -0.86 (0.41), residues: 431 helix: 2.33 (0.50), residues: 116 sheet: -1.28 (0.40), residues: 151 loop : -1.99 (0.46), residues: 164 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 0.012 0.001 PHE H 70 TYR 0.012 0.001 TYR H 80 ARG 0.002 0.000 ARG C 282 *********************** 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 83 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7503 (tptm) cc_final: 0.7194 (ttpt) REVERT: C 80 LYS cc_start: 0.7800 (mmmt) cc_final: 0.7560 (mttt) REVERT: C 222 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7646 (mt-10) REVERT: C 289 MET cc_start: 0.9255 (tpt) cc_final: 0.8452 (tpt) REVERT: H 32 TYR cc_start: 0.8756 (m-80) cc_final: 0.8403 (m-80) REVERT: H 63 ASP cc_start: 0.7944 (t0) cc_final: 0.7733 (t0) REVERT: L 18 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8106 (m) outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.1463 time to fit residues: 14.5922 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.0170 chunk 7 optimal weight: 0.4980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.149500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124832 restraints weight = 4783.175| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.23 r_work: 0.3391 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3505 Z= 0.178 Angle : 0.515 6.588 4747 Z= 0.274 Chirality : 0.041 0.154 550 Planarity : 0.003 0.032 593 Dihedral : 4.664 25.371 466 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.64 % Allowed : 19.33 % Favored : 76.03 % 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: -0.69 (0.42), residues: 431 helix: 2.48 (0.50), residues: 116 sheet: -1.18 (0.41), residues: 149 loop : -1.88 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS C 159 PHE 0.010 0.001 PHE H 70 TYR 0.013 0.001 TYR H 80 ARG 0.002 0.000 ARG C 282 *********************** 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 89 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7477 (tptm) cc_final: 0.7172 (ttpt) REVERT: C 80 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7585 (mttt) REVERT: C 222 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 289 MET cc_start: 0.9252 (tpt) cc_final: 0.8412 (tpt) REVERT: H 32 TYR cc_start: 0.8747 (m-80) cc_final: 0.8343 (m-80) REVERT: L 18 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8072 (m) REVERT: L 79 GLN cc_start: 0.8038 (mt0) cc_final: 0.7726 (mt0) REVERT: L 81 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7892 (pm20) outliers start: 18 outliers final: 15 residues processed: 85 average time/residue: 0.1559 time to fit residues: 16.6602 Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 THR 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 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: 0.8980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.145407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120587 restraints weight = 4704.038| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.20 r_work: 0.3351 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3505 Z= 0.268 Angle : 0.582 7.211 4747 Z= 0.308 Chirality : 0.042 0.154 550 Planarity : 0.003 0.025 593 Dihedral : 4.898 23.423 466 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.93 % Allowed : 19.33 % Favored : 74.74 % 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: -0.65 (0.42), residues: 431 helix: 2.30 (0.50), residues: 116 sheet: -1.00 (0.40), residues: 157 loop : -1.87 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS C 159 PHE 0.012 0.001 PHE L 91 TYR 0.015 0.002 TYR H 80 ARG 0.002 0.001 ARG C 282 *********************** 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 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.397 Fit side-chains REVERT: C 77 LYS cc_start: 0.7508 (tptm) cc_final: 0.7208 (ttpt) REVERT: C 80 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7644 (mttt) REVERT: C 222 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 289 MET cc_start: 0.9281 (tpt) cc_final: 0.8476 (tpt) REVERT: H 32 TYR cc_start: 0.8727 (m-80) cc_final: 0.8287 (m-80) REVERT: L 18 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.8006 (m) REVERT: L 81 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7827 (pm20) outliers start: 23 outliers final: 18 residues processed: 78 average time/residue: 0.1619 time to fit residues: 15.5615 Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 220 VAL Chi-restraints excluded: chain C residue 245 THR 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 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 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU 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: 0.8980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.149409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124906 restraints weight = 4775.489| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.20 r_work: 0.3397 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3505 Z= 0.168 Angle : 0.507 6.314 4747 Z= 0.269 Chirality : 0.040 0.153 550 Planarity : 0.003 0.030 593 Dihedral : 4.523 22.391 466 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.64 % Allowed : 20.88 % 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: -0.45 (0.42), residues: 431 helix: 2.54 (0.50), residues: 116 sheet: -0.79 (0.42), residues: 147 loop : -1.88 (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 C 159 PHE 0.009 0.001 PHE H 70 TYR 0.013 0.001 TYR H 80 ARG 0.002 0.000 ARG C 282 *********************** 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 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7467 (tptm) cc_final: 0.7200 (ttpt) REVERT: C 80 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7598 (mttt) REVERT: C 222 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 289 MET cc_start: 0.9261 (tpt) cc_final: 0.8384 (tpt) REVERT: H 32 TYR cc_start: 0.8694 (m-80) cc_final: 0.8289 (m-80) REVERT: L 81 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7864 (pm20) outliers start: 18 outliers final: 15 residues processed: 79 average time/residue: 0.1611 time to fit residues: 15.7320 Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 48 MET 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 25 SER Chi-restraints excluded: chain L residue 42 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: 0.5980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 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 = 0.3798 r_free = 0.3798 target = 0.146078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121526 restraints weight = 4684.657| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.20 r_work: 0.3352 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3505 Z= 0.246 Angle : 0.562 6.878 4747 Z= 0.297 Chirality : 0.042 0.154 550 Planarity : 0.003 0.027 593 Dihedral : 4.726 22.870 466 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.90 % Allowed : 20.88 % Favored : 74.23 % 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: -0.41 (0.42), residues: 431 helix: 2.41 (0.50), residues: 116 sheet: -0.74 (0.42), residues: 155 loop : -1.78 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS C 159 PHE 0.012 0.001 PHE L 91 TYR 0.016 0.002 TYR H 80 ARG 0.002 0.000 ARG C 282 *********************** 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 83 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.387 Fit side-chains REVERT: C 77 LYS cc_start: 0.7490 (tptm) cc_final: 0.7224 (ttpt) REVERT: C 80 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7638 (mttt) REVERT: C 222 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7635 (mt-10) REVERT: C 289 MET cc_start: 0.9267 (tpt) cc_final: 0.8474 (tpt) REVERT: H 32 TYR cc_start: 0.8728 (m-80) cc_final: 0.8327 (m-80) REVERT: L 81 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8098 (pt0) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.1561 time to fit residues: 14.9121 Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 C residue 308 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 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 25 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.0030 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 2 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4288 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.146858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122449 restraints weight = 4764.115| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.23 r_work: 0.3382 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3505 Z= 0.191 Angle : 0.525 6.328 4747 Z= 0.278 Chirality : 0.041 0.153 550 Planarity : 0.003 0.027 593 Dihedral : 4.551 22.727 466 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.12 % Allowed : 22.42 % Favored : 73.45 % 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: -0.33 (0.42), residues: 431 helix: 2.51 (0.50), residues: 116 sheet: -0.62 (0.43), residues: 148 loop : -1.82 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.009 0.001 PHE H 70 TYR 0.015 0.001 TYR H 80 ARG 0.002 0.000 ARG H 98 ********************** 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 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.363 Fit side-chains REVERT: C 77 LYS cc_start: 0.7446 (tptm) cc_final: 0.7198 (ttpt) REVERT: C 222 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 289 MET cc_start: 0.9240 (tpt) cc_final: 0.8356 (tpt) REVERT: H 32 TYR cc_start: 0.8705 (m-80) cc_final: 0.8328 (m-80) REVERT: L 81 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8094 (pt0) outliers start: 16 outliers final: 15 residues processed: 74 average time/residue: 0.1444 time to fit residues: 13.3628 Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 25 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 GLU 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: 0.3980 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.145720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121314 restraints weight = 4799.289| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.21 r_work: 0.3348 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3505 Z= 0.244 Angle : 0.561 6.850 4747 Z= 0.296 Chirality : 0.042 0.153 550 Planarity : 0.003 0.028 593 Dihedral : 4.703 23.178 466 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.15 % Allowed : 21.13 % Favored : 73.71 % 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: -0.33 (0.43), residues: 431 helix: 2.39 (0.49), residues: 116 sheet: -0.58 (0.43), residues: 155 loop : -1.80 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS C 159 PHE 0.012 0.001 PHE L 91 TYR 0.016 0.002 TYR H 80 ARG 0.002 0.000 ARG C 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.79 seconds wall clock time: 44 minutes 43.74 seconds (2683.74 seconds total)