Starting phenix.real_space_refine on Thu Jul 24 04:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p75_17518/07_2025/8p75_17518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p75_17518/07_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_17518/07_2025/8p75_17518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p75_17518/07_2025/8p75_17518.map" model { file = "/net/cci-nas-00/data/ceres_data/8p75_17518/07_2025/8p75_17518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p75_17518/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.97, per 1000 atoms: 1.54 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.87 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: 1.63 Time building geometry restraints manager: 2.10 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: 337.600 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.480 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:16.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 378.260 ------------------------------------------------------------------------------- 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 : 0.911 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 1.8541 time to fit residues: 177.0726 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 : 0.639 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157769 restraints weight = 4391.189| |-----------------------------------------------------------------------------| r_work (start): 0.3874 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: 0.7658 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 : 0.640 Fit side-chains REVERT: I 186 ILE cc_start: 0.7891 (pp) cc_final: 0.7516 (pp) REVERT: I 192 ASP cc_start: 0.6545 (t70) cc_final: 0.6277 (t70) outliers start: 13 outliers final: 4 residues processed: 101 average time/residue: 1.4161 time to fit residues: 148.4408 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 : 0.547 ------------------------------------------------------------------------------- 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: 0.0070 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.177574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156091 restraints weight = 4416.366| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 0.98 r_work: 0.3754 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5228 Z= 0.166 Angle : 0.590 8.523 7076 Z= 0.308 Chirality : 0.042 0.138 777 Planarity : 0.005 0.046 903 Dihedral : 6.132 57.024 708 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.37 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: 1.67 (0.33), residues: 618 helix: 1.96 (0.28), residues: 343 sheet: 2.92 (1.43), residues: 9 loop : -0.05 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.007 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.003 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 278) hydrogen bonds : angle 4.74961 ( 780) covalent geometry : bond 0.00373 ( 5228) covalent geometry : angle 0.59035 ( 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 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.572 Fit side-chains REVERT: I 16 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7054 (mm-30) REVERT: I 186 ILE cc_start: 0.7937 (pp) cc_final: 0.7489 (pp) REVERT: I 192 ASP cc_start: 0.6594 (t70) cc_final: 0.6327 (t70) REVERT: I 229 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: J 273 GLN cc_start: 0.7226 (tp40) cc_final: 0.6958 (tp40) outliers start: 14 outliers final: 6 residues processed: 100 average time/residue: 1.4794 time to fit residues: 153.0656 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 10.0000 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.179097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157516 restraints weight = 4600.343| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.01 r_work: 0.3768 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.0869 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= 0.127 Angle : 0.536 9.404 7076 Z= 0.279 Chirality : 0.040 0.134 777 Planarity : 0.004 0.047 903 Dihedral : 5.796 55.461 708 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.07 % Allowed : 16.06 % Favored : 80.87 % 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: 1.84 (0.34), residues: 618 helix: 2.11 (0.28), residues: 343 sheet: 3.08 (1.46), residues: 9 loop : 0.00 (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 110 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 278) hydrogen bonds : angle 4.55724 ( 780) covalent geometry : bond 0.00282 ( 5228) covalent geometry : angle 0.53605 ( 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 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.590 Fit side-chains REVERT: I 16 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6917 (mm-30) REVERT: I 186 ILE cc_start: 0.7891 (pp) cc_final: 0.7457 (pp) REVERT: I 192 ASP cc_start: 0.6525 (t70) cc_final: 0.6250 (t0) REVERT: I 229 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6155 (tm-30) REVERT: J 99 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6613 (tp30) REVERT: J 273 GLN cc_start: 0.7238 (tp40) cc_final: 0.6973 (tp40) outliers start: 17 outliers final: 6 residues processed: 103 average time/residue: 1.3930 time to fit residues: 148.8110 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 : 0.723 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 275 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 = 0.4105 r_free = 0.4105 target = 0.176610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155468 restraints weight = 4432.366| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 0.96 r_work: 0.3743 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5228 Z= 0.210 Angle : 0.650 10.378 7076 Z= 0.337 Chirality : 0.044 0.143 777 Planarity : 0.005 0.044 903 Dihedral : 6.248 57.689 708 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 18.23 % Favored : 79.78 % 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: 1.45 (0.33), residues: 618 helix: 1.77 (0.28), residues: 343 sheet: 3.44 (1.56), residues: 9 loop : -0.15 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.022 0.003 TYR I 207 ARG 0.003 0.001 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.05553 ( 278) hydrogen bonds : angle 4.84220 ( 780) covalent geometry : bond 0.00476 ( 5228) covalent geometry : angle 0.64968 ( 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.564 Fit side-chains REVERT: I 186 ILE cc_start: 0.8014 (pp) cc_final: 0.7494 (pp) REVERT: I 192 ASP cc_start: 0.6594 (t70) cc_final: 0.6333 (t70) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 1.4188 time to fit residues: 141.5021 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 216 ASP Chi-restraints excluded: chain J residue 231 THR 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: 5.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ** 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 = 0.4101 r_free = 0.4101 target = 0.176440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155350 restraints weight = 4389.509| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 0.95 r_work: 0.3741 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5228 Z= 0.213 Angle : 0.668 11.924 7076 Z= 0.347 Chirality : 0.045 0.146 777 Planarity : 0.005 0.039 903 Dihedral : 6.316 57.424 708 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.35 % Allowed : 17.87 % Favored : 79.78 % 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: 1.29 (0.33), residues: 618 helix: 1.63 (0.27), residues: 343 sheet: 3.67 (1.58), residues: 9 loop : -0.22 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.008 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.027 0.003 TYR I 207 ARG 0.004 0.001 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.05593 ( 278) hydrogen bonds : angle 4.87245 ( 780) covalent geometry : bond 0.00484 ( 5228) covalent geometry : angle 0.66813 ( 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.605 Fit side-chains REVERT: I 186 ILE cc_start: 0.8035 (pp) cc_final: 0.7520 (pp) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 1.4298 time to fit residues: 141.0058 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 231 THR 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: 0.7980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 ** 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 = 0.179489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158218 restraints weight = 4497.039| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 0.99 r_work: 0.3778 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5228 Z= 0.122 Angle : 0.574 14.433 7076 Z= 0.292 Chirality : 0.040 0.138 777 Planarity : 0.004 0.048 903 Dihedral : 5.659 54.546 708 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.81 % Allowed : 18.59 % 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: 1.84 (0.34), residues: 618 helix: 2.10 (0.28), residues: 343 sheet: 3.64 (1.60), residues: 9 loop : 0.02 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.017 0.001 PHE I 110 TYR 0.024 0.002 TYR I 207 ARG 0.002 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 278) hydrogen bonds : angle 4.51842 ( 780) covalent geometry : bond 0.00276 ( 5228) covalent geometry : angle 0.57418 ( 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.609 Fit side-chains REVERT: I 16 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6924 (mm-30) REVERT: I 186 ILE cc_start: 0.7960 (pp) cc_final: 0.7474 (pp) REVERT: I 192 ASP cc_start: 0.6486 (t70) cc_final: 0.6189 (t0) outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 1.5319 time to fit residues: 153.7191 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 247 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 = 0.4103 r_free = 0.4103 target = 0.176487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155360 restraints weight = 4380.428| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 0.94 r_work: 0.3742 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5228 Z= 0.221 Angle : 0.686 7.213 7076 Z= 0.357 Chirality : 0.045 0.144 777 Planarity : 0.005 0.040 903 Dihedral : 6.236 57.632 708 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.81 % Allowed : 18.23 % Favored : 79.96 % 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: 1.35 (0.33), residues: 618 helix: 1.64 (0.27), residues: 343 sheet: 3.76 (1.61), residues: 9 loop : -0.15 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.021 0.003 TYR I 91 ARG 0.003 0.001 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.05609 ( 278) hydrogen bonds : angle 4.88374 ( 780) covalent geometry : bond 0.00505 ( 5228) covalent geometry : angle 0.68561 ( 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 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.533 Fit side-chains REVERT: H 254 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: I 186 ILE cc_start: 0.8011 (pp) cc_final: 0.7531 (pp) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 1.4324 time to fit residues: 138.0189 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 254 GLU 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 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: 3.9990 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 136 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 = 0.4116 r_free = 0.4116 target = 0.177773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156385 restraints weight = 4354.717| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 0.97 r_work: 0.3754 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5228 Z= 0.162 Angle : 0.645 14.315 7076 Z= 0.329 Chirality : 0.042 0.142 777 Planarity : 0.005 0.042 903 Dihedral : 5.975 56.293 708 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 18.41 % 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: 1.50 (0.34), residues: 618 helix: 1.79 (0.27), residues: 343 sheet: 3.54 (1.57), residues: 9 loop : -0.10 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE I 110 TYR 0.020 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 278) hydrogen bonds : angle 4.72943 ( 780) covalent geometry : bond 0.00371 ( 5228) covalent geometry : angle 0.64496 ( 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.598 Fit side-chains REVERT: I 186 ILE cc_start: 0.7982 (pp) cc_final: 0.7507 (pp) REVERT: I 192 ASP cc_start: 0.6573 (t70) cc_final: 0.6285 (t70) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 1.5310 time to fit residues: 138.1369 Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 130 GLN ** 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 = 0.4117 r_free = 0.4117 target = 0.177705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156257 restraints weight = 4365.895| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 0.97 r_work: 0.3754 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5228 Z= 0.170 Angle : 0.680 19.236 7076 Z= 0.342 Chirality : 0.043 0.141 777 Planarity : 0.005 0.042 903 Dihedral : 5.998 56.654 708 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % 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: 1.47 (0.33), residues: 618 helix: 1.76 (0.27), residues: 343 sheet: 3.59 (1.57), residues: 9 loop : -0.09 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.007 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.003 0.001 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 278) hydrogen bonds : angle 4.73368 ( 780) covalent geometry : bond 0.00392 ( 5228) covalent geometry : angle 0.68007 ( 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: 12 poor density : 81 time to evaluate : 0.830 Fit side-chains REVERT: I 186 ILE cc_start: 0.7987 (pp) cc_final: 0.7515 (pp) REVERT: I 192 ASP cc_start: 0.6568 (t70) cc_final: 0.6284 (t70) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 1.5466 time to fit residues: 140.9091 Evaluate side-chains 86 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 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 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: 3.9990 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 130 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.177770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156340 restraints weight = 4381.947| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.97 r_work: 0.3756 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5228 Z= 0.164 Angle : 0.630 7.727 7076 Z= 0.328 Chirality : 0.042 0.141 777 Planarity : 0.005 0.042 903 Dihedral : 5.933 56.489 708 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 18.77 % Favored : 79.24 % 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: 1.49 (0.33), residues: 618 helix: 1.76 (0.27), residues: 343 sheet: 3.52 (1.57), residues: 9 loop : -0.08 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 PHE 0.015 0.002 PHE I 110 TYR 0.020 0.002 TYR I 91 ARG 0.003 0.000 ARG J 188 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 278) hydrogen bonds : angle 4.72271 ( 780) covalent geometry : bond 0.00378 ( 5228) covalent geometry : angle 0.63010 ( 7076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5960.31 seconds wall clock time: 103 minutes 7.09 seconds (6187.09 seconds total)