Starting phenix.real_space_refine on Wed Mar 5 20:02:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz4_37946/03_2025/8wz4_37946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz4_37946/03_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_37946/03_2025/8wz4_37946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz4_37946/03_2025/8wz4_37946.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz4_37946/03_2025/8wz4_37946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz4_37946/03_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-5624/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: 3.25, per 1000 atoms: 0.94 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: 0.86 Conformation dependent library (CDL) restraints added in 432.7 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: 0.37 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: 0.77 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 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: 2.890 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.490 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.190 ------------------------------------------------------------------------------- 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 : 0.325 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1618 time to fit residues: 22.0112 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 : 0.366 ------------------------------------------------------------------------------- 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 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 : 0.371 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: 0.1819 time to fit residues: 16.7140 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 : 0.492 ------------------------------------------------------------------------------- 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: 0.0770 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 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: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.148481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123785 restraints weight = 4613.188| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.17 r_work: 0.3380 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3505 Z= 0.230 Angle : 0.588 7.884 4747 Z= 0.308 Chirality : 0.043 0.159 550 Planarity : 0.003 0.028 593 Dihedral : 5.192 41.279 466 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.35 % Allowed : 17.01 % 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: -1.45 (0.40), residues: 431 helix: 1.82 (0.49), residues: 116 sheet: -1.77 (0.38), residues: 148 loop : -2.14 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS C 159 PHE 0.013 0.002 PHE H 70 TYR 0.011 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 86 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.328 Fit side-chains REVERT: C 77 LYS cc_start: 0.7675 (tptm) cc_final: 0.7232 (ttpt) REVERT: C 80 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7540 (mttt) REVERT: C 222 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7431 (mt-10) REVERT: C 289 MET cc_start: 0.9175 (tpt) cc_final: 0.8558 (tpt) REVERT: H 32 TYR cc_start: 0.8774 (m-80) cc_final: 0.8520 (m-80) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.1471 time to fit residues: 14.8585 Evaluate side-chains 73 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 GLN C 302 GLN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120940 restraints weight = 4713.459| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.20 r_work: 0.3347 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3505 Z= 0.282 Angle : 0.602 7.869 4747 Z= 0.315 Chirality : 0.043 0.153 550 Planarity : 0.003 0.026 593 Dihedral : 5.266 37.252 466 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.64 % Allowed : 17.78 % 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: -1.17 (0.41), residues: 431 helix: 1.91 (0.49), residues: 116 sheet: -1.51 (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 H 47 HIS 0.004 0.002 HIS L 90 PHE 0.012 0.002 PHE L 91 TYR 0.017 0.002 TYR C 86 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 87 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7552 (tptm) cc_final: 0.7222 (ttpt) REVERT: C 80 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7576 (mttt) REVERT: C 222 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7506 (mt-10) REVERT: C 289 MET cc_start: 0.9215 (tpt) cc_final: 0.8608 (tpt) REVERT: H 32 TYR cc_start: 0.8768 (m-80) cc_final: 0.8370 (m-80) REVERT: H 63 ASP cc_start: 0.7976 (t0) cc_final: 0.7746 (t0) REVERT: L 18 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8113 (m) outliers start: 18 outliers final: 14 residues processed: 81 average time/residue: 0.1450 time to fit residues: 14.5451 Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 0.7980 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.145897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121036 restraints weight = 4777.148| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.22 r_work: 0.3345 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3505 Z= 0.277 Angle : 0.595 7.642 4747 Z= 0.310 Chirality : 0.043 0.181 550 Planarity : 0.003 0.024 593 Dihedral : 5.128 32.949 466 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.38 % Allowed : 19.85 % Favored : 75.77 % 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: 2.03 (0.50), residues: 116 sheet: -1.28 (0.39), residues: 156 loop : -2.00 (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 H 70 TYR 0.019 0.002 TYR C 86 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 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: C 77 LYS cc_start: 0.7497 (tptm) cc_final: 0.7207 (ttpt) REVERT: C 80 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7603 (mttt) REVERT: C 222 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 289 MET cc_start: 0.9260 (tpt) cc_final: 0.8502 (tpt) REVERT: H 32 TYR cc_start: 0.8766 (m-80) cc_final: 0.8395 (m-80) REVERT: H 63 ASP cc_start: 0.8017 (t0) cc_final: 0.7815 (t0) REVERT: L 18 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8016 (m) REVERT: L 54 LEU cc_start: 0.8576 (pp) cc_final: 0.8349 (tt) outliers start: 17 outliers final: 14 residues processed: 74 average time/residue: 0.1543 time to fit residues: 14.2088 Evaluate side-chains 74 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 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 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=3.00 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121336 restraints weight = 4820.288| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.18 r_work: 0.3361 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3505 Z= 0.243 Angle : 0.560 7.189 4747 Z= 0.296 Chirality : 0.042 0.150 550 Planarity : 0.003 0.024 593 Dihedral : 4.955 27.623 466 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.67 % Allowed : 19.59 % 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: -0.85 (0.41), residues: 431 helix: 2.15 (0.50), residues: 116 sheet: -1.20 (0.40), residues: 154 loop : -1.89 (0.47), residues: 161 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 H 70 TYR 0.019 0.002 TYR C 86 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 88 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.387 Fit side-chains REVERT: C 77 LYS cc_start: 0.7453 (tptm) cc_final: 0.7174 (ttpt) REVERT: C 80 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7624 (mttt) REVERT: C 222 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7523 (mt-10) REVERT: C 289 MET cc_start: 0.9268 (tpt) cc_final: 0.8427 (tpt) REVERT: H 32 TYR cc_start: 0.8746 (m-80) cc_final: 0.8375 (m-80) REVERT: H 63 ASP cc_start: 0.8027 (t0) cc_final: 0.7823 (t0) REVERT: L 18 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8038 (m) REVERT: L 81 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7872 (pm20) outliers start: 22 outliers final: 16 residues processed: 82 average time/residue: 0.1466 time to fit residues: 15.0307 Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 18 VAL 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 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: 0.6980 chunk 27 optimal weight: 0.3980 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: 0.2980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.147047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122513 restraints weight = 4687.084| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.18 r_work: 0.3362 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3505 Z= 0.231 Angle : 0.543 7.004 4747 Z= 0.289 Chirality : 0.042 0.152 550 Planarity : 0.003 0.026 593 Dihedral : 4.824 23.311 466 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.15 % Allowed : 20.36 % 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: -0.74 (0.42), residues: 431 helix: 2.47 (0.50), residues: 110 sheet: -1.08 (0.41), residues: 155 loop : -1.92 (0.47), residues: 166 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 0.011 0.001 PHE H 70 TYR 0.020 0.002 TYR C 86 ARG 0.002 0.000 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 83 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.392 Fit side-chains REVERT: C 77 LYS cc_start: 0.7461 (tptm) cc_final: 0.7213 (ttpt) REVERT: C 222 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7586 (mt-10) REVERT: C 289 MET cc_start: 0.9287 (tpt) cc_final: 0.8403 (tpt) REVERT: H 32 TYR cc_start: 0.8740 (m-80) cc_final: 0.8318 (m-80) REVERT: L 18 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8064 (m) REVERT: L 54 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8268 (tt) REVERT: L 81 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7870 (pm20) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.1741 time to fit residues: 16.4522 Evaluate side-chains 76 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 18 VAL 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 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 54 LEU 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: 0.4980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.144405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119581 restraints weight = 4817.267| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.23 r_work: 0.3342 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3505 Z= 0.262 Angle : 0.571 7.127 4747 Z= 0.303 Chirality : 0.042 0.152 550 Planarity : 0.003 0.023 593 Dihedral : 4.847 23.781 466 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.41 % Allowed : 20.62 % Favored : 73.97 % 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: -0.74 (0.41), residues: 431 helix: 2.42 (0.50), residues: 110 sheet: -1.02 (0.41), residues: 155 loop : -1.96 (0.46), residues: 166 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 0.002 PHE L 91 TYR 0.020 0.002 TYR C 86 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 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.384 Fit side-chains REVERT: C 77 LYS cc_start: 0.7422 (tptm) cc_final: 0.7221 (ttpt) REVERT: C 289 MET cc_start: 0.9299 (tpt) cc_final: 0.8435 (tpt) REVERT: H 32 TYR cc_start: 0.8738 (m-80) cc_final: 0.8321 (m-80) REVERT: L 18 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8055 (m) REVERT: L 81 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8060 (pt0) outliers start: 21 outliers final: 17 residues processed: 74 average time/residue: 0.1419 time to fit residues: 13.3787 Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 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 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 C residue 308 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 VAL 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 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 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: 0.4980 chunk 19 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.146354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121766 restraints weight = 4691.897| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.21 r_work: 0.3372 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3505 Z= 0.206 Angle : 0.536 6.497 4747 Z= 0.285 Chirality : 0.041 0.153 550 Planarity : 0.003 0.027 593 Dihedral : 4.662 23.090 466 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.90 % Allowed : 21.65 % 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: -0.54 (0.42), residues: 431 helix: 2.55 (0.50), residues: 110 sheet: -0.86 (0.42), residues: 155 loop : -1.86 (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 0.009 0.001 PHE L 91 TYR 0.018 0.002 TYR C 86 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 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.392 Fit side-chains REVERT: C 289 MET cc_start: 0.9278 (tpt) cc_final: 0.8391 (tpt) REVERT: H 32 TYR cc_start: 0.8715 (m-80) cc_final: 0.8318 (m-80) REVERT: L 81 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8063 (pt0) outliers start: 19 outliers final: 16 residues processed: 74 average time/residue: 0.1437 time to fit residues: 13.4011 Evaluate side-chains 76 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 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 25 SER Chi-restraints excluded: chain L residue 52 LYS 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: 1.9990 chunk 19 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 23 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.2954 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.144126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121020 restraints weight = 4703.121| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.06 r_work: 0.3357 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3505 Z= 0.167 Angle : 0.515 6.254 4747 Z= 0.275 Chirality : 0.041 0.154 550 Planarity : 0.003 0.031 593 Dihedral : 4.489 22.626 466 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.38 % Allowed : 22.68 % 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: -0.38 (0.42), residues: 431 helix: 2.76 (0.50), residues: 110 sheet: -0.67 (0.44), residues: 147 loop : -1.88 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS C 159 PHE 0.010 0.001 PHE H 70 TYR 0.015 0.002 TYR C 86 ARG 0.001 0.000 ARG C 282 ********************** 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 75 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.399 Fit side-chains REVERT: C 289 MET cc_start: 0.9202 (tpt) cc_final: 0.8305 (tpt) REVERT: H 32 TYR cc_start: 0.8659 (m-80) cc_final: 0.8264 (m-80) outliers start: 17 outliers final: 16 residues processed: 70 average time/residue: 0.1363 time to fit residues: 12.1592 Evaluate side-chains 73 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 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 25 SER Chi-restraints excluded: chain L residue 52 LYS 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: 0.1980 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.141643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118391 restraints weight = 4774.341| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.09 r_work: 0.3317 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3505 Z= 0.243 Angle : 0.557 6.810 4747 Z= 0.294 Chirality : 0.042 0.153 550 Planarity : 0.003 0.033 593 Dihedral : 4.657 23.151 466 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.12 % Allowed : 22.94 % 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: -0.46 (0.42), residues: 431 helix: 2.54 (0.50), residues: 110 sheet: -0.73 (0.43), residues: 155 loop : -1.84 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.011 0.002 PHE L 91 TYR 0.017 0.002 TYR C 86 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: 2524.43 seconds wall clock time: 44 minutes 14.77 seconds (2654.77 seconds total)