Starting phenix.real_space_refine on Wed Sep 17 05:24:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p74_17517/09_2025/8p74_17517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p74_17517/09_2025/8p74_17517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p74_17517/09_2025/8p74_17517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p74_17517/09_2025/8p74_17517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p74_17517/09_2025/8p74_17517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p74_17517/09_2025/8p74_17517.map" } resolution = 2.2 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 30 5.16 5 C 3267 2.51 5 N 864 2.21 5 O 953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5115 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: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Unusual residues: {'ACE': 1} Classifications: {'peptide': 275, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260} Chain breaks: 2 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Time building chain proxies: 1.63, per 1000 atoms: 0.32 Number of scatterers: 5115 At special positions: 0 Unit cell: (84.075, 94.05, 66.975, 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 30 16.00 O 953 8.00 N 864 7.00 C 3267 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: 0.47 Conformation dependent library (CDL) restraints added in 204.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 62.6% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.649A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (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 Processing helix chain 'I' and resid 49 through 71 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.924A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.621A 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: 4.670A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.543A 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: 3.520A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.156A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 261 Processing helix chain 'I' and resid 266 through 283 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: 4.316A 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 removed outlier: 3.619A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) 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: 3.683A 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: 7.086A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.162A 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 134 273 hydrogen bonds defined for protein. 762 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: 0.69 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: 1663 1.37 - 1.51: 1490 1.51 - 1.65: 1992 1.65 - 1.80: 18 1.80 - 1.94: 30 Bond restraints: 5193 Sorted by residual: bond pdb=" C08 X3Z J 401 " pdb=" N09 X3Z J 401 " ideal model delta sigma weight residual 1.340 1.457 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C19 X3Z J 401 " pdb=" N20 X3Z J 401 " ideal model delta sigma weight residual 1.351 1.458 -0.107 2.00e-02 2.50e+03 2.87e+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 1.46e+01 bond pdb=" N06 X3Z J 401 " pdb=" N07 X3Z J 401 " ideal model delta sigma weight residual 1.343 1.406 -0.063 2.00e-02 2.50e+03 9.83e+00 bond pdb=" C16 X3Z J 401 " pdb="BR17 X3Z J 401 " ideal model delta sigma weight residual 1.896 1.938 -0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 5188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 6849 1.57 - 3.14: 136 3.14 - 4.71: 34 4.71 - 6.29: 8 6.29 - 7.86: 2 Bond angle restraints: 7029 Sorted by residual: angle pdb=" N VAL J 210 " pdb=" CA VAL J 210 " pdb=" C VAL J 210 " ideal model delta sigma weight residual 109.19 106.12 3.07 8.20e-01 1.49e+00 1.40e+01 angle pdb=" C VAL J 210 " pdb=" CA VAL J 210 " pdb=" CB VAL J 210 " ideal model delta sigma weight residual 109.33 112.61 -3.28 9.80e-01 1.04e+00 1.12e+01 angle pdb=" CA VAL J 210 " pdb=" C VAL J 210 " pdb=" N PRO J 211 " ideal model delta sigma weight residual 116.57 119.74 -3.17 9.80e-01 1.04e+00 1.05e+01 angle pdb=" CB GLU I 49 " pdb=" CG GLU I 49 " pdb=" CD GLU I 49 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.70e+00 3.46e-01 6.54e+00 angle pdb=" CB ARG I 63 " pdb=" CG ARG I 63 " pdb=" CD ARG I 63 " ideal model delta sigma weight residual 111.30 116.79 -5.49 2.30e+00 1.89e-01 5.70e+00 ... (remaining 7024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2730 17.83 - 35.66: 294 35.66 - 53.49: 81 53.49 - 71.32: 24 71.32 - 89.15: 10 Dihedral angle restraints: 3139 sinusoidal: 1305 harmonic: 1834 Sorted by residual: 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 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU H 262 " pdb=" CG GLU H 262 " pdb=" CD GLU H 262 " pdb=" OE1 GLU H 262 " ideal model delta sinusoidal sigma weight residual 0.00 89.15 -89.15 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU J 126 " pdb=" CG GLU J 126 " pdb=" CD GLU J 126 " pdb=" OE1 GLU J 126 " ideal model delta sinusoidal sigma weight residual 0.00 89.07 -89.07 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 460 0.029 - 0.058: 202 0.058 - 0.087: 71 0.087 - 0.117: 31 0.117 - 0.146: 8 Chirality restraints: 772 Sorted by residual: 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 2.59 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA VAL I 120 " pdb=" N VAL I 120 " pdb=" C VAL I 120 " pdb=" CB VAL I 120 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-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 4.27e-01 ... (remaining 769 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 231 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO J 232 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO J 232 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 232 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO I 166 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 71 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO J 72 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 72 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 72 " -0.022 5.00e-02 4.00e+02 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 360 2.74 - 3.28: 5269 3.28 - 3.82: 9404 3.82 - 4.36: 11233 4.36 - 4.90: 18312 Nonbonded interactions: 44578 Sorted by model distance: nonbonded pdb=" N GLU J 147 " pdb=" OE1 GLU J 147 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.208 3.040 nonbonded pdb=" O ARG J 283 " pdb=" O HOH J 502 " model vdw 2.228 3.040 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.270 3.040 nonbonded pdb=" NZ LYS I 114 " pdb=" O ILE J 55 " model vdw 2.297 3.120 ... (remaining 44573 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: 5.150 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 0.117 5193 Z= 0.201 Angle : 0.598 7.858 7029 Z= 0.301 Chirality : 0.041 0.146 772 Planarity : 0.005 0.044 897 Dihedral : 16.962 89.149 1951 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 0.91 % Allowed : 17.64 % Favored : 81.45 % 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 (0.35), residues: 612 helix: 1.91 (0.29), residues: 332 sheet: -0.15 (0.94), residues: 29 loop : 0.50 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 63 TYR 0.017 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5193) covalent geometry : angle 0.59797 ( 7029) hydrogen bonds : bond 0.12961 ( 273) hydrogen bonds : angle 5.64125 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.216 Fit side-chains REVERT: J 147 GLU cc_start: 0.7215 (pm20) cc_final: 0.6806 (pt0) outliers start: 5 outliers final: 5 residues processed: 93 average time/residue: 0.7035 time to fit residues: 67.7385 Evaluate side-chains 89 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 124 GLN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.163485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144448 restraints weight = 4695.990| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.06 r_work: 0.3615 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5193 Z= 0.173 Angle : 0.597 7.522 7029 Z= 0.305 Chirality : 0.043 0.156 772 Planarity : 0.005 0.043 897 Dihedral : 8.506 78.453 709 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 2.73 % Allowed : 14.18 % Favored : 83.09 % 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: 1.77 (0.34), residues: 612 helix: 1.79 (0.28), residues: 341 sheet: 0.92 (1.20), residues: 19 loop : 0.47 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 63 TYR 0.020 0.002 TYR I 91 PHE 0.018 0.002 PHE I 30 TRP 0.011 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5193) covalent geometry : angle 0.59678 ( 7029) hydrogen bonds : bond 0.05097 ( 273) hydrogen bonds : angle 4.76037 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.190 Fit side-chains REVERT: I 260 LYS cc_start: 0.7138 (tttm) cc_final: 0.6932 (ttpp) REVERT: J 99 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6618 (tt0) REVERT: J 169 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.6437 (m-80) outliers start: 15 outliers final: 5 residues processed: 94 average time/residue: 0.6460 time to fit residues: 63.0847 Evaluate side-chains 89 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144369 restraints weight = 4640.296| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.05 r_work: 0.3614 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5193 Z= 0.177 Angle : 0.601 7.582 7029 Z= 0.305 Chirality : 0.044 0.156 772 Planarity : 0.005 0.042 897 Dihedral : 7.928 78.812 703 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 3.27 % Allowed : 13.27 % Favored : 83.45 % 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: 1.69 (0.34), residues: 612 helix: 1.74 (0.28), residues: 341 sheet: 0.89 (1.23), residues: 19 loop : 0.40 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 63 TYR 0.020 0.002 TYR I 91 PHE 0.020 0.002 PHE I 30 TRP 0.012 0.002 TRP J 132 HIS 0.005 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5193) covalent geometry : angle 0.60145 ( 7029) hydrogen bonds : bond 0.05075 ( 273) hydrogen bonds : angle 4.71529 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.203 Fit side-chains REVERT: H 249 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7102 (mt0) REVERT: I 260 LYS cc_start: 0.7157 (tttm) cc_final: 0.6947 (ttpp) REVERT: J 11 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.4597 (tpt170) REVERT: J 14 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6914 (tttm) REVERT: J 99 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: J 169 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: J 293 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7820 (mptt) outliers start: 18 outliers final: 6 residues processed: 101 average time/residue: 0.7080 time to fit residues: 73.9880 Evaluate side-chains 99 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145171 restraints weight = 4632.607| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.06 r_work: 0.3625 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5193 Z= 0.152 Angle : 0.573 7.157 7029 Z= 0.291 Chirality : 0.042 0.152 772 Planarity : 0.005 0.041 897 Dihedral : 7.521 77.654 703 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 3.27 % Allowed : 13.82 % Favored : 82.91 % 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: 1.77 (0.34), residues: 612 helix: 1.85 (0.28), residues: 341 sheet: 0.69 (1.21), residues: 19 loop : 0.39 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 63 TYR 0.019 0.002 TYR I 91 PHE 0.019 0.002 PHE I 30 TRP 0.011 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5193) covalent geometry : angle 0.57350 ( 7029) hydrogen bonds : bond 0.04729 ( 273) hydrogen bonds : angle 4.62239 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.252 Fit side-chains REVERT: H 249 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7110 (mt0) REVERT: I 260 LYS cc_start: 0.7152 (tttm) cc_final: 0.6933 (ttpp) REVERT: J 11 ARG cc_start: 0.4875 (OUTLIER) cc_final: 0.4559 (tpt170) REVERT: J 99 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: J 169 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: J 293 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7818 (mptt) outliers start: 18 outliers final: 8 residues processed: 99 average time/residue: 0.6892 time to fit residues: 70.7456 Evaluate side-chains 99 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143704 restraints weight = 4744.481| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.07 r_work: 0.3610 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5193 Z= 0.193 Angle : 0.627 7.801 7029 Z= 0.318 Chirality : 0.045 0.162 772 Planarity : 0.006 0.042 897 Dihedral : 7.492 79.143 703 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 4.18 % Allowed : 12.73 % Favored : 83.09 % 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: 1.50 (0.33), residues: 612 helix: 1.61 (0.27), residues: 341 sheet: 0.63 (1.22), residues: 19 loop : 0.30 (0.39), residues: 252 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 0.022 0.002 PHE I 30 TRP 0.012 0.002 TRP I 11 HIS 0.006 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5193) covalent geometry : angle 0.62689 ( 7029) hydrogen bonds : bond 0.05151 ( 273) hydrogen bonds : angle 4.72153 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.215 Fit side-chains REVERT: H 249 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: I 242 ARG cc_start: 0.4749 (OUTLIER) cc_final: 0.4441 (mmt180) REVERT: I 260 LYS cc_start: 0.7166 (tttm) cc_final: 0.6956 (ttpp) REVERT: J 11 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.4596 (tpt170) REVERT: J 14 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6800 (tttm) REVERT: J 99 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: J 293 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7796 (mptt) outliers start: 23 outliers final: 8 residues processed: 104 average time/residue: 0.6657 time to fit residues: 71.6727 Evaluate side-chains 101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 242 ARG Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 293 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.164636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145961 restraints weight = 4729.404| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.05 r_work: 0.3638 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5193 Z= 0.124 Angle : 0.546 7.029 7029 Z= 0.278 Chirality : 0.041 0.154 772 Planarity : 0.005 0.041 897 Dihedral : 7.045 76.353 703 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.55 % Allowed : 14.18 % Favored : 83.27 % 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: 1.80 (0.34), residues: 612 helix: 1.94 (0.28), residues: 341 sheet: 0.55 (1.20), residues: 19 loop : 0.31 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 63 TYR 0.017 0.002 TYR I 91 PHE 0.020 0.002 PHE I 30 TRP 0.009 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5193) covalent geometry : angle 0.54635 ( 7029) hydrogen bonds : bond 0.04334 ( 273) hydrogen bonds : angle 4.50751 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.216 Fit side-chains REVERT: I 260 LYS cc_start: 0.7111 (tttm) cc_final: 0.6896 (ttpp) REVERT: J 14 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6848 (tttm) REVERT: J 99 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6588 (tt0) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 0.6759 time to fit residues: 68.6118 Evaluate side-chains 91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 7 optimal weight: 0.2980 chunk 52 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148305 restraints weight = 4896.138| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.08 r_work: 0.3673 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5193 Z= 0.098 Angle : 0.496 5.939 7029 Z= 0.256 Chirality : 0.040 0.149 772 Planarity : 0.004 0.044 897 Dihedral : 6.694 74.007 703 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 1.82 % Allowed : 15.64 % Favored : 82.55 % 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: 2.11 (0.35), residues: 612 helix: 2.22 (0.29), residues: 338 sheet: 0.44 (1.10), residues: 19 loop : 0.45 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 63 TYR 0.014 0.001 TYR I 60 PHE 0.018 0.001 PHE J 252 TRP 0.007 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5193) covalent geometry : angle 0.49642 ( 7029) hydrogen bonds : bond 0.03722 ( 273) hydrogen bonds : angle 4.28764 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.219 Fit side-chains REVERT: I 260 LYS cc_start: 0.7064 (tttm) cc_final: 0.6862 (ttpp) REVERT: J 99 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6514 (tt0) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.7056 time to fit residues: 71.6491 Evaluate side-chains 88 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 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 244 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145573 restraints weight = 4776.399| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.06 r_work: 0.3630 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5193 Z= 0.144 Angle : 0.561 6.809 7029 Z= 0.288 Chirality : 0.042 0.151 772 Planarity : 0.005 0.040 897 Dihedral : 6.833 77.280 702 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.73 % Allowed : 16.00 % Favored : 81.27 % 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: 1.95 (0.34), residues: 612 helix: 2.05 (0.28), residues: 341 sheet: 0.65 (1.18), residues: 19 loop : 0.39 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 63 TYR 0.018 0.002 TYR I 91 PHE 0.018 0.002 PHE I 30 TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5193) covalent geometry : angle 0.56084 ( 7029) hydrogen bonds : bond 0.04458 ( 273) hydrogen bonds : angle 4.43475 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.222 Fit side-chains REVERT: I 260 LYS cc_start: 0.7128 (tttm) cc_final: 0.6922 (ttpp) REVERT: J 14 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6822 (tttm) REVERT: J 99 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6623 (tt0) outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 0.6755 time to fit residues: 65.1049 Evaluate side-chains 91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145437 restraints weight = 4828.480| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.07 r_work: 0.3627 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5193 Z= 0.144 Angle : 0.566 7.721 7029 Z= 0.289 Chirality : 0.042 0.153 772 Planarity : 0.005 0.040 897 Dihedral : 6.822 77.097 702 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 2.18 % Allowed : 16.18 % Favored : 81.64 % 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: 1.85 (0.34), residues: 612 helix: 1.97 (0.28), residues: 341 sheet: 0.72 (1.19), residues: 19 loop : 0.34 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 63 TYR 0.018 0.002 TYR I 91 PHE 0.018 0.002 PHE I 30 TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5193) covalent geometry : angle 0.56554 ( 7029) hydrogen bonds : bond 0.04497 ( 273) hydrogen bonds : angle 4.48938 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.230 Fit side-chains REVERT: I 260 LYS cc_start: 0.7128 (tttm) cc_final: 0.6920 (ttpp) REVERT: J 14 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6831 (tttm) REVERT: J 99 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6618 (tt0) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 0.6740 time to fit residues: 63.6523 Evaluate side-chains 90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147245 restraints weight = 4874.762| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.07 r_work: 0.3651 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5193 Z= 0.110 Angle : 0.529 7.248 7029 Z= 0.272 Chirality : 0.041 0.155 772 Planarity : 0.005 0.042 897 Dihedral : 6.680 74.920 702 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 1.27 % Allowed : 17.45 % Favored : 81.27 % 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: 2.01 (0.34), residues: 612 helix: 2.13 (0.28), residues: 341 sheet: 0.75 (1.14), residues: 19 loop : 0.36 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 63 TYR 0.015 0.002 TYR I 91 PHE 0.020 0.002 PHE J 252 TRP 0.008 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 5193) covalent geometry : angle 0.52851 ( 7029) hydrogen bonds : bond 0.04010 ( 273) hydrogen bonds : angle 4.37490 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.210 Fit side-chains REVERT: I 228 MET cc_start: 0.7628 (ptm) cc_final: 0.7418 (ptp) REVERT: I 260 LYS cc_start: 0.7106 (tttm) cc_final: 0.6904 (ttpp) REVERT: J 14 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6772 (tttm) REVERT: J 99 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6565 (tt0) outliers start: 7 outliers final: 3 residues processed: 86 average time/residue: 0.6352 time to fit residues: 56.7772 Evaluate side-chains 84 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 244 CYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 0.0000 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 119 ASN I 247 GLN J 148 ASN ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.166856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147828 restraints weight = 4878.907| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.08 r_work: 0.3656 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5193 Z= 0.105 Angle : 0.517 6.894 7029 Z= 0.265 Chirality : 0.040 0.150 772 Planarity : 0.005 0.042 897 Dihedral : 6.649 74.519 702 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 1.45 % Allowed : 17.27 % Favored : 81.27 % 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: 2.11 (0.34), residues: 612 helix: 2.23 (0.28), residues: 341 sheet: 0.90 (1.14), residues: 19 loop : 0.36 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 63 TYR 0.015 0.001 TYR I 91 PHE 0.019 0.002 PHE J 252 TRP 0.008 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 5193) covalent geometry : angle 0.51714 ( 7029) hydrogen bonds : bond 0.03845 ( 273) hydrogen bonds : angle 4.30679 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2565.18 seconds wall clock time: 44 minutes 31.51 seconds (2671.51 seconds total)