Starting phenix.real_space_refine on Fri Oct 10 12:38:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p75_17518/10_2025/8p75_17518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p75_17518/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p75_17518/10_2025/8p75_17518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p75_17518/10_2025/8p75_17518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p75_17518/10_2025/8p75_17518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p75_17518/10_2025/8p75_17518.map" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.30 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: 0.44 Conformation dependent library (CDL) restraints added in 191.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.18 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: 0.81 Time building geometry restraints manager: 0.61 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG J 188 TYR 0.018 0.002 TYR I 91 PHE 0.015 0.002 PHE I 30 TRP 0.011 0.002 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5228) covalent geometry : angle 0.59141 ( 7076) hydrogen bonds : bond 0.13426 ( 278) hydrogen bonds : angle 5.72637 ( 780) *********************** 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 : 0.221 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.6720 time to fit residues: 64.1107 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 : 0.222 ------------------------------------------------------------------------------- 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 54 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.178949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157920 restraints weight = 4455.195| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 0.96 r_work: 0.3776 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0641 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= 0.128 Angle : 0.540 8.022 7076 Z= 0.283 Chirality : 0.040 0.131 777 Planarity : 0.004 0.045 903 Dihedral : 6.373 55.273 714 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.34), residues: 618 helix: 2.16 (0.28), residues: 342 sheet: 2.82 (1.34), residues: 9 loop : 0.10 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 77 TYR 0.018 0.002 TYR I 91 PHE 0.014 0.002 PHE I 110 TRP 0.008 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5228) covalent geometry : angle 0.54007 ( 7076) hydrogen bonds : bond 0.04809 ( 278) hydrogen bonds : angle 4.72242 ( 780) *********************** 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 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.139 Fit side-chains REVERT: I 192 ASP cc_start: 0.6511 (t70) cc_final: 0.6252 (t70) outliers start: 13 outliers final: 4 residues processed: 100 average time/residue: 0.6731 time to fit residues: 69.5710 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 42 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.180015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158690 restraints weight = 4505.184| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 0.99 r_work: 0.3784 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.0829 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= 0.115 Angle : 0.514 8.265 7076 Z= 0.267 Chirality : 0.039 0.130 777 Planarity : 0.004 0.046 903 Dihedral : 5.712 54.879 708 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.34), residues: 618 helix: 2.23 (0.28), residues: 343 sheet: 1.40 (1.24), residues: 15 loop : 0.12 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 63 TYR 0.017 0.001 TYR I 91 PHE 0.013 0.001 PHE I 110 TRP 0.008 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5228) covalent geometry : angle 0.51407 ( 7076) hydrogen bonds : bond 0.04422 ( 278) hydrogen bonds : angle 4.53581 ( 780) *********************** 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 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.149 Fit side-chains REVERT: I 186 ILE cc_start: 0.7903 (pp) cc_final: 0.7502 (pp) REVERT: I 192 ASP cc_start: 0.6532 (t70) cc_final: 0.6259 (t0) REVERT: I 229 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.6165 (tm-30) REVERT: J 99 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6620 (tp30) outliers start: 16 outliers final: 6 residues processed: 105 average time/residue: 0.6910 time to fit residues: 74.9434 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 47 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 183 ASN I 275 GLN J 83 HIS J 105 ASN ** 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 = 0.4117 r_free = 0.4117 target = 0.178082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156595 restraints weight = 4454.549| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 0.99 r_work: 0.3754 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5228 Z= 0.160 Angle : 0.592 9.070 7076 Z= 0.305 Chirality : 0.042 0.136 777 Planarity : 0.004 0.042 903 Dihedral : 5.996 56.860 708 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.34), residues: 618 helix: 2.04 (0.28), residues: 342 sheet: 3.13 (1.48), residues: 9 loop : -0.08 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 63 TYR 0.020 0.002 TYR I 91 PHE 0.015 0.002 PHE I 30 TRP 0.010 0.002 TRP H 306 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5228) covalent geometry : angle 0.59177 ( 7076) hydrogen bonds : bond 0.05067 ( 278) hydrogen bonds : angle 4.69402 ( 780) *********************** 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: 14 poor density : 93 time to evaluate : 0.222 Fit side-chains REVERT: I 35 VAL cc_start: 0.7208 (t) cc_final: 0.6956 (p) REVERT: I 138 LYS cc_start: 0.6763 (ptpp) cc_final: 0.6453 (pptt) REVERT: I 186 ILE cc_start: 0.7948 (pp) cc_final: 0.7448 (pp) REVERT: I 192 ASP cc_start: 0.6619 (t70) cc_final: 0.6348 (t70) REVERT: I 229 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6092 (tm-30) REVERT: J 99 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6781 (tp30) outliers start: 14 outliers final: 6 residues processed: 102 average time/residue: 0.6707 time to fit residues: 70.7870 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 57 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 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 J 83 HIS J 105 ASN ** 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 = 0.4103 r_free = 0.4103 target = 0.176570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155435 restraints weight = 4465.050| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 0.96 r_work: 0.3743 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1014 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= 0.211 Angle : 0.667 10.568 7076 Z= 0.343 Chirality : 0.045 0.143 777 Planarity : 0.005 0.042 903 Dihedral : 6.293 57.680 708 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 2.17 % Allowed : 17.69 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.33), residues: 618 helix: 1.74 (0.27), residues: 342 sheet: 3.41 (1.54), residues: 9 loop : -0.18 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 77 TYR 0.021 0.003 TYR I 91 PHE 0.016 0.002 PHE I 30 TRP 0.012 0.003 TRP J 132 HIS 0.009 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 5228) covalent geometry : angle 0.66670 ( 7076) hydrogen bonds : bond 0.05619 ( 278) hydrogen bonds : angle 4.89094 ( 780) *********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.212 Fit side-chains REVERT: I 138 LYS cc_start: 0.6840 (ptpp) cc_final: 0.6588 (pptt) REVERT: I 186 ILE cc_start: 0.8004 (pp) cc_final: 0.7487 (pp) REVERT: J 189 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7227 (tpt) outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 0.6483 time to fit residues: 63.1559 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU 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 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 4 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 105 ASN ** 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 = 0.4123 r_free = 0.4123 target = 0.178774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157322 restraints weight = 4604.356| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.00 r_work: 0.3765 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5228 Z= 0.131 Angle : 0.573 12.935 7076 Z= 0.291 Chirality : 0.040 0.136 777 Planarity : 0.004 0.046 903 Dihedral : 5.815 55.618 708 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.34), residues: 618 helix: 2.03 (0.28), residues: 342 sheet: 3.46 (1.55), residues: 9 loop : -0.10 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 77 TYR 0.019 0.002 TYR I 91 PHE 0.015 0.002 PHE I 110 TRP 0.010 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5228) covalent geometry : angle 0.57334 ( 7076) hydrogen bonds : bond 0.04638 ( 278) hydrogen bonds : angle 4.60751 ( 780) *********************** 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 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.208 Fit side-chains REVERT: I 35 VAL cc_start: 0.7218 (t) cc_final: 0.6994 (p) REVERT: I 186 ILE cc_start: 0.7952 (pp) cc_final: 0.7472 (pp) REVERT: I 192 ASP cc_start: 0.6554 (t70) cc_final: 0.6272 (t0) REVERT: J 273 GLN cc_start: 0.7418 (tt0) cc_final: 0.7145 (tp40) outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.6771 time to fit residues: 73.5051 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 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 = 0.4137 r_free = 0.4137 target = 0.180017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158766 restraints weight = 4431.155| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 0.98 r_work: 0.3783 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5228 Z= 0.121 Angle : 0.569 15.238 7076 Z= 0.287 Chirality : 0.040 0.134 777 Planarity : 0.004 0.047 903 Dihedral : 5.571 54.833 708 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.53 % Allowed : 17.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.34), residues: 618 helix: 2.19 (0.28), residues: 342 sheet: 3.15 (1.47), residues: 9 loop : 0.00 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.022 0.002 TYR I 207 PHE 0.015 0.001 PHE I 110 TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5228) covalent geometry : angle 0.56897 ( 7076) hydrogen bonds : bond 0.04380 ( 278) hydrogen bonds : angle 4.53204 ( 780) *********************** 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 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.223 Fit side-chains REVERT: I 186 ILE cc_start: 0.7937 (pp) cc_final: 0.7484 (pp) REVERT: I 192 ASP cc_start: 0.6536 (t70) cc_final: 0.6238 (t0) REVERT: J 273 GLN cc_start: 0.7418 (tt0) cc_final: 0.7148 (tp40) outliers start: 14 outliers final: 6 residues processed: 94 average time/residue: 0.6927 time to fit residues: 67.4365 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 : 0.205 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN J 83 HIS ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.179065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157733 restraints weight = 4496.991| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 0.99 r_work: 0.3772 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1107 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= 0.135 Angle : 0.564 5.974 7076 Z= 0.293 Chirality : 0.041 0.134 777 Planarity : 0.005 0.047 903 Dihedral : 5.659 55.611 708 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.81 % Allowed : 18.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.34), residues: 618 helix: 2.12 (0.28), residues: 342 sheet: 2.81 (1.47), residues: 9 loop : -0.03 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 11 TYR 0.019 0.002 TYR I 91 PHE 0.015 0.002 PHE I 110 TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5228) covalent geometry : angle 0.56407 ( 7076) hydrogen bonds : bond 0.04604 ( 278) hydrogen bonds : angle 4.59780 ( 780) *********************** 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 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.223 Fit side-chains REVERT: I 186 ILE cc_start: 0.7929 (pp) cc_final: 0.7495 (pp) REVERT: I 192 ASP cc_start: 0.6566 (t70) cc_final: 0.6282 (t0) REVERT: J 273 GLN cc_start: 0.7422 (tt0) cc_final: 0.7152 (tp40) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.6594 time to fit residues: 62.9353 Evaluate side-chains 88 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 35 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 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 247 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 = 0.4131 r_free = 0.4131 target = 0.179067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157783 restraints weight = 4438.313| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 0.98 r_work: 0.3773 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1172 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= 0.139 Angle : 0.606 13.858 7076 Z= 0.306 Chirality : 0.041 0.134 777 Planarity : 0.004 0.047 903 Dihedral : 5.645 55.710 708 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.81 % Allowed : 18.05 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.34), residues: 618 helix: 2.09 (0.28), residues: 342 sheet: 2.72 (1.48), residues: 9 loop : -0.02 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 279 TYR 0.019 0.002 TYR I 91 PHE 0.014 0.002 PHE I 110 TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5228) covalent geometry : angle 0.60640 ( 7076) hydrogen bonds : bond 0.04614 ( 278) hydrogen bonds : angle 4.60916 ( 780) *********************** 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 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.214 Fit side-chains REVERT: I 35 VAL cc_start: 0.7256 (t) cc_final: 0.6998 (p) REVERT: I 186 ILE cc_start: 0.7938 (pp) cc_final: 0.7509 (pp) REVERT: I 192 ASP cc_start: 0.6518 (t70) cc_final: 0.6228 (t0) REVERT: J 273 GLN cc_start: 0.7413 (tt0) cc_final: 0.7129 (tp40) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.7092 time to fit residues: 65.4318 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 0.0570 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.178440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156981 restraints weight = 4439.061| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 0.99 r_work: 0.3764 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5228 Z= 0.153 Angle : 0.651 19.832 7076 Z= 0.323 Chirality : 0.041 0.135 777 Planarity : 0.005 0.044 903 Dihedral : 5.724 56.205 708 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.99 % Allowed : 18.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.34), residues: 618 helix: 2.00 (0.27), residues: 342 sheet: 2.85 (1.48), residues: 9 loop : -0.03 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 279 TYR 0.019 0.002 TYR I 91 PHE 0.014 0.002 PHE I 30 TRP 0.009 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5228) covalent geometry : angle 0.65056 ( 7076) hydrogen bonds : bond 0.04789 ( 278) hydrogen bonds : angle 4.66125 ( 780) ********************** 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 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.210 Fit side-chains REVERT: I 35 VAL cc_start: 0.7255 (t) cc_final: 0.6986 (p) REVERT: I 186 ILE cc_start: 0.7939 (pp) cc_final: 0.7519 (pp) REVERT: I 192 ASP cc_start: 0.6536 (t70) cc_final: 0.6246 (t70) REVERT: J 99 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6577 (tp30) REVERT: J 273 GLN cc_start: 0.7417 (tt0) cc_final: 0.7131 (tp40) outliers start: 11 outliers final: 6 residues processed: 89 average time/residue: 0.6861 time to fit residues: 63.3286 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 0.0770 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 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 = 0.4132 r_free = 0.4132 target = 0.178890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157542 restraints weight = 4469.126| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 0.99 r_work: 0.3771 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5228 Z= 0.137 Angle : 0.584 8.810 7076 Z= 0.302 Chirality : 0.041 0.134 777 Planarity : 0.004 0.045 903 Dihedral : 5.622 55.621 708 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.34), residues: 618 helix: 2.05 (0.27), residues: 342 sheet: 2.84 (1.44), residues: 9 loop : -0.02 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 279 TYR 0.019 0.002 TYR I 91 PHE 0.015 0.002 PHE I 110 TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5228) covalent geometry : angle 0.58417 ( 7076) hydrogen bonds : bond 0.04598 ( 278) hydrogen bonds : angle 4.61453 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.72 seconds wall clock time: 49 minutes 13.38 seconds (2953.38 seconds total)