Starting phenix.real_space_refine on Sat May 10 05:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p75_17518/05_2025/8p75_17518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p75_17518/05_2025/8p75_17518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p75_17518/05_2025/8p75_17518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p75_17518/05_2025/8p75_17518.map" model { file = "/net/cci-nas-00/data/ceres_data/8p75_17518/05_2025/8p75_17518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p75_17518/05_2025/8p75_17518.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 31 5.16 5 C 3289 2.51 5 N 869 2.21 5 O 991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5181 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'X3Z': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Time building chain proxies: 5.27, per 1000 atoms: 1.02 Number of scatterers: 5181 At special positions: 0 Unit cell: (83.3625, 93.3375, 66.2625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 31 16.00 O 991 8.00 N 869 7.00 C 3289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.37 Conformation dependent library (CDL) restraints added in 627.9 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 62.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.521A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.821A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.599A pdb=" N GLY I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.864A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.722A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.718A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.737A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 207 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.763A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.423A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 Processing helix chain 'J' and resid 217 through 229 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.910A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 14 through 20 removed outlier: 6.882A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 278 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 1673 1.37 - 1.51: 1484 1.51 - 1.65: 2021 1.65 - 1.80: 22 1.80 - 1.94: 28 Bond restraints: 5228 Sorted by residual: bond pdb=" C08 X3Z J 401 " pdb=" N09 X3Z J 401 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C19 X3Z J 401 " pdb=" N20 X3Z J 401 " ideal model delta sigma weight residual 1.351 1.454 -0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C29 X3Z J 401 " pdb=" N07 X3Z J 401 " ideal model delta sigma weight residual 1.376 1.300 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" N06 X3Z J 401 " pdb=" N07 X3Z J 401 " ideal model delta sigma weight residual 1.343 1.403 -0.060 2.00e-02 2.50e+03 9.00e+00 bond pdb=" C16 X3Z J 401 " pdb="BR17 X3Z J 401 " ideal model delta sigma weight residual 1.896 1.940 -0.044 2.00e-02 2.50e+03 4.82e+00 ... (remaining 5223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 6832 1.32 - 2.63: 173 2.63 - 3.95: 50 3.95 - 5.26: 15 5.26 - 6.58: 6 Bond angle restraints: 7076 Sorted by residual: angle pdb=" CA ARG J 11 " pdb=" CB ARG J 11 " pdb=" CG ARG J 11 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA ILE I 186 " pdb=" CB ILE I 186 " pdb=" CG1 ILE I 186 " ideal model delta sigma weight residual 110.40 114.48 -4.08 1.70e+00 3.46e-01 5.76e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.60 4.30 1.80e+00 3.09e-01 5.70e+00 angle pdb=" CB ARG J 11 " pdb=" CG ARG J 11 " pdb=" CD ARG J 11 " ideal model delta sigma weight residual 111.30 116.63 -5.33 2.30e+00 1.89e-01 5.36e+00 angle pdb=" CB ILE I 186 " pdb=" CG1 ILE I 186 " pdb=" CD1 ILE I 186 " ideal model delta sigma weight residual 113.80 118.57 -4.77 2.10e+00 2.27e-01 5.17e+00 ... (remaining 7071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 2752 17.58 - 35.16: 301 35.16 - 52.74: 87 52.74 - 70.32: 15 70.32 - 87.89: 9 Dihedral angle restraints: 3164 sinusoidal: 1317 harmonic: 1847 Sorted by residual: dihedral pdb=" CG ARG J 179 " pdb=" CD ARG J 179 " pdb=" NE ARG J 179 " pdb=" CZ ARG J 179 " ideal model delta sinusoidal sigma weight residual 180.00 135.86 44.14 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB GLU I 137 " pdb=" CG GLU I 137 " pdb=" CD GLU I 137 " pdb=" OE1 GLU I 137 " ideal model delta sinusoidal sigma weight residual 0.00 85.05 -85.05 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 164.43 15.57 0 5.00e+00 4.00e-02 9.70e+00 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 540 0.035 - 0.069: 159 0.069 - 0.104: 58 0.104 - 0.138: 19 0.138 - 0.173: 1 Chirality restraints: 777 Sorted by residual: chirality pdb=" C21 X3Z J 401 " pdb=" C22 X3Z J 401 " pdb=" C24 X3Z J 401 " pdb=" N20 X3Z J 401 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 132 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO I 133 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO I 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 133 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 194 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C PHE I 194 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE I 194 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU I 195 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 193 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ASP I 193 " -0.020 2.00e-02 2.50e+03 pdb=" O ASP I 193 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE I 194 " 0.007 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 413 2.74 - 3.28: 5373 3.28 - 3.82: 9627 3.82 - 4.36: 11364 4.36 - 4.90: 18837 Nonbonded interactions: 45614 Sorted by model distance: nonbonded pdb=" OD1 ASP J 137 " pdb=" NZ LYS J 139 " model vdw 2.198 3.120 nonbonded pdb=" N GLU J 147 " pdb=" OE1 GLU J 147 " model vdw 2.218 3.120 nonbonded pdb=" O LEU I 144 " pdb=" O HOH I 401 " model vdw 2.246 3.040 nonbonded pdb=" O HOH I 412 " pdb=" O HOH I 429 " model vdw 2.305 3.040 nonbonded pdb=" O HOH J 520 " pdb=" O HOH J 523 " model vdw 2.314 3.040 ... (remaining 45609 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: 3.620 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.440 Find NCS groups from input model: 0.080 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:15.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.004 0.111 5228 Z= 0.190 Angle : 0.591 6.575 7076 Z= 0.296 Chirality : 0.041 0.173 777 Planarity : 0.004 0.042 903 Dihedral : 16.475 87.895 1968 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 18.77 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.61 (0.33), residues: 618 helix: 1.88 (0.28), residues: 340 sheet: 2.46 (1.28), residues: 15 loop : -0.06 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.13426 ( 278) hydrogen bonds : angle 5.72637 ( 780) covalent geometry : bond 0.00403 ( 5228) covalent geometry : angle 0.59141 ( 7076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.612 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 1.4258 time to fit residues: 135.8583 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 216 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN J 83 HIS J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.178763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157807 restraints weight = 4391.190| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 0.95 r_work: 0.3773 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5228 Z= 0.131 Angle : 0.545 7.856 7076 Z= 0.285 Chirality : 0.040 0.132 777 Planarity : 0.004 0.045 903 Dihedral : 6.369 55.313 714 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.35 % Allowed : 16.25 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.88 (0.34), residues: 618 helix: 2.12 (0.28), residues: 343 sheet: 2.79 (1.35), residues: 9 loop : 0.10 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 278) hydrogen bonds : angle 4.71252 ( 780) covalent geometry : bond 0.00288 ( 5228) covalent geometry : angle 0.54464 ( 7076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.641 Fit side-chains REVERT: I 186 ILE cc_start: 0.7892 (pp) cc_final: 0.7517 (pp) REVERT: I 192 ASP cc_start: 0.6544 (t70) cc_final: 0.6276 (t70) outliers start: 13 outliers final: 4 residues processed: 101 average time/residue: 1.6415 time to fit residues: 171.9870 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 0.0170 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 275 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.178437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157270 restraints weight = 4472.728| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 0.96 r_work: 0.3766 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5228 Z= 0.141 Angle : 0.554 8.423 7076 Z= 0.289 Chirality : 0.041 0.134 777 Planarity : 0.004 0.046 903 Dihedral : 5.950 56.170 708 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 16.43 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.81 (0.34), residues: 618 helix: 2.08 (0.28), residues: 343 sheet: 2.94 (1.40), residues: 9 loop : 0.01 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 278) hydrogen bonds : angle 4.65130 ( 780) covalent geometry : bond 0.00314 ( 5228) covalent geometry : angle 0.55429 ( 7076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.587 Fit side-chains REVERT: I 16 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6955 (mm-30) REVERT: I 186 ILE cc_start: 0.7917 (pp) cc_final: 0.7482 (pp) REVERT: I 192 ASP cc_start: 0.6600 (t70) cc_final: 0.6325 (t70) REVERT: I 229 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6167 (tm-30) outliers start: 14 outliers final: 6 residues processed: 100 average time/residue: 1.5344 time to fit residues: 158.5141 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 275 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.180322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159216 restraints weight = 4615.824| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 0.98 r_work: 0.3790 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5228 Z= 0.112 Angle : 0.514 9.855 7076 Z= 0.265 Chirality : 0.039 0.131 777 Planarity : 0.004 0.047 903 Dihedral : 5.590 54.676 708 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.89 % Allowed : 15.88 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.99 (0.34), residues: 618 helix: 2.24 (0.28), residues: 343 sheet: 1.36 (1.27), residues: 15 loop : 0.12 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.001 PHE I 110 TYR 0.017 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 278) hydrogen bonds : angle 4.45404 ( 780) covalent geometry : bond 0.00250 ( 5228) covalent geometry : angle 0.51411 ( 7076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.593 Fit side-chains REVERT: I 186 ILE cc_start: 0.7860 (pp) cc_final: 0.7406 (pp) REVERT: I 192 ASP cc_start: 0.6505 (t70) cc_final: 0.6232 (t0) REVERT: I 229 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: J 99 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6589 (tp30) outliers start: 16 outliers final: 4 residues processed: 100 average time/residue: 1.4300 time to fit residues: 148.1522 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 136 GLN I 183 ASN I 247 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.179002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157496 restraints weight = 4588.691| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.01 r_work: 0.3767 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5228 Z= 0.132 Angle : 0.545 10.766 7076 Z= 0.280 Chirality : 0.040 0.133 777 Planarity : 0.004 0.045 903 Dihedral : 5.718 58.334 708 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.17 % Allowed : 16.79 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.86 (0.34), residues: 618 helix: 2.14 (0.28), residues: 342 sheet: 3.22 (1.51), residues: 9 loop : -0.01 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.013 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.002 0.000 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 278) hydrogen bonds : angle 4.55598 ( 780) covalent geometry : bond 0.00296 ( 5228) covalent geometry : angle 0.54548 ( 7076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.582 Fit side-chains REVERT: I 186 ILE cc_start: 0.7887 (pp) cc_final: 0.7435 (pp) REVERT: I 192 ASP cc_start: 0.6560 (t70) cc_final: 0.6287 (t0) REVERT: J 99 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6598 (tp30) REVERT: J 273 GLN cc_start: 0.7219 (tp40) cc_final: 0.6956 (tp40) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 1.5160 time to fit residues: 148.9029 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 275 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155912 restraints weight = 4505.526| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 0.99 r_work: 0.3749 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5228 Z= 0.172 Angle : 0.608 11.552 7076 Z= 0.312 Chirality : 0.042 0.138 777 Planarity : 0.005 0.044 903 Dihedral : 5.972 57.668 708 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.53 % Allowed : 17.87 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.67 (0.34), residues: 618 helix: 1.99 (0.28), residues: 342 sheet: 3.48 (1.56), residues: 9 loop : -0.09 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.008 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.002 0.001 ARG J 136 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 278) hydrogen bonds : angle 4.68997 ( 780) covalent geometry : bond 0.00391 ( 5228) covalent geometry : angle 0.60841 ( 7076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.684 Fit side-chains REVERT: I 186 ILE cc_start: 0.7938 (pp) cc_final: 0.7500 (pp) REVERT: I 192 ASP cc_start: 0.6599 (t70) cc_final: 0.6331 (t70) REVERT: J 189 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7233 (tpt) outliers start: 14 outliers final: 7 residues processed: 95 average time/residue: 1.4522 time to fit residues: 142.9168 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 18 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.158055 restraints weight = 4495.484| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 0.99 r_work: 0.3775 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5228 Z= 0.124 Angle : 0.567 15.973 7076 Z= 0.284 Chirality : 0.040 0.135 777 Planarity : 0.004 0.047 903 Dihedral : 5.628 57.913 708 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.35 % Allowed : 18.23 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.90 (0.34), residues: 618 helix: 2.18 (0.28), residues: 342 sheet: 3.42 (1.54), residues: 9 loop : 0.01 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.014 0.001 PHE I 110 TYR 0.018 0.002 TYR I 91 ARG 0.002 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 278) hydrogen bonds : angle 4.50518 ( 780) covalent geometry : bond 0.00280 ( 5228) covalent geometry : angle 0.56677 ( 7076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.638 Fit side-chains REVERT: I 192 ASP cc_start: 0.6535 (t70) cc_final: 0.6265 (t0) REVERT: J 189 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7246 (tpt) outliers start: 13 outliers final: 7 residues processed: 92 average time/residue: 1.5611 time to fit residues: 148.4793 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 189 MET Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 18 GLN I 183 ASN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.179640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158751 restraints weight = 4490.564| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.96 r_work: 0.3785 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5228 Z= 0.122 Angle : 0.537 5.697 7076 Z= 0.279 Chirality : 0.040 0.133 777 Planarity : 0.004 0.045 903 Dihedral : 5.536 57.637 708 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.17 % Allowed : 18.41 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.91 (0.34), residues: 618 helix: 2.19 (0.28), residues: 342 sheet: 3.22 (1.49), residues: 9 loop : 0.03 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.013 0.001 PHE I 110 TYR 0.027 0.002 TYR I 207 ARG 0.002 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 278) hydrogen bonds : angle 4.52022 ( 780) covalent geometry : bond 0.00275 ( 5228) covalent geometry : angle 0.53659 ( 7076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.676 Fit side-chains REVERT: I 186 ILE cc_start: 0.8139 (pp) cc_final: 0.7458 (pp) REVERT: I 192 ASP cc_start: 0.6516 (t70) cc_final: 0.6246 (t0) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 1.6353 time to fit residues: 157.7845 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 18 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157993 restraints weight = 4381.817| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 0.98 r_work: 0.3776 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5228 Z= 0.137 Angle : 0.587 13.848 7076 Z= 0.299 Chirality : 0.041 0.133 777 Planarity : 0.004 0.046 903 Dihedral : 5.628 59.815 708 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.35 % Allowed : 18.59 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.81 (0.34), residues: 618 helix: 2.10 (0.28), residues: 342 sheet: 2.88 (1.48), residues: 9 loop : -0.01 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.014 0.002 PHE I 110 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 278) hydrogen bonds : angle 4.56434 ( 780) covalent geometry : bond 0.00314 ( 5228) covalent geometry : angle 0.58693 ( 7076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.522 Fit side-chains REVERT: I 186 ILE cc_start: 0.8145 (pp) cc_final: 0.7459 (pp) REVERT: I 192 ASP cc_start: 0.6530 (t70) cc_final: 0.6244 (t0) REVERT: J 147 GLU cc_start: 0.6974 (pm20) cc_final: 0.6712 (pt0) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 1.4877 time to fit residues: 148.0099 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 18 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.179225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157847 restraints weight = 4410.535| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 0.98 r_work: 0.3774 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5228 Z= 0.143 Angle : 0.635 19.776 7076 Z= 0.315 Chirality : 0.041 0.133 777 Planarity : 0.004 0.047 903 Dihedral : 5.657 59.900 708 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.81 % Allowed : 19.31 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.77 (0.34), residues: 618 helix: 2.03 (0.28), residues: 343 sheet: 2.96 (1.48), residues: 9 loop : 0.03 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.013 0.002 PHE I 110 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 278) hydrogen bonds : angle 4.58469 ( 780) covalent geometry : bond 0.00328 ( 5228) covalent geometry : angle 0.63479 ( 7076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.618 Fit side-chains REVERT: I 186 ILE cc_start: 0.8147 (pp) cc_final: 0.7466 (pp) REVERT: I 192 ASP cc_start: 0.6481 (t70) cc_final: 0.6198 (t70) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 1.4981 time to fit residues: 135.0414 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN I 18 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156779 restraints weight = 4423.449| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 0.95 r_work: 0.3761 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5228 Z= 0.171 Angle : 0.629 9.743 7076 Z= 0.326 Chirality : 0.043 0.138 777 Planarity : 0.005 0.048 903 Dihedral : 5.869 59.753 708 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 19.49 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.59 (0.34), residues: 618 helix: 1.86 (0.27), residues: 343 sheet: 3.05 (1.50), residues: 9 loop : -0.02 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.008 0.001 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.003 0.001 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 278) hydrogen bonds : angle 4.70970 ( 780) covalent geometry : bond 0.00390 ( 5228) covalent geometry : angle 0.62910 ( 7076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5371.54 seconds wall clock time: 93 minutes 9.37 seconds (5589.37 seconds total)