Starting phenix.real_space_refine on Sat May 10 04:47:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p74_17517/05_2025/8p74_17517.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p74_17517/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p74_17517/05_2025/8p74_17517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p74_17517/05_2025/8p74_17517.map" model { file = "/net/cci-nas-00/data/ceres_data/8p74_17517/05_2025/8p74_17517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p74_17517/05_2025/8p74_17517.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.14, per 1000 atoms: 0.81 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: 1.39 Conformation dependent library (CDL) restraints added in 597.2 milliseconds 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: 0.55 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: 1.44 Time building geometry restraints manager: 1.53 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: 7.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.820 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (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 TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.12961 ( 273) hydrogen bonds : angle 5.64125 ( 762) covalent geometry : bond 0.00432 ( 5193) covalent geometry : angle 0.59797 ( 7029) *********************** 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 : 0.685 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: 1.3415 time to fit residues: 129.5283 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 : 0.589 ------------------------------------------------------------------------------- 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 51 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145888 restraints weight = 4943.185| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.10 r_work: 0.3634 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0610 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= 0.130 Angle : 0.539 6.384 7029 Z= 0.277 Chirality : 0.041 0.155 772 Planarity : 0.005 0.040 897 Dihedral : 8.437 77.693 709 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 2.18 % Allowed : 14.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.35), residues: 612 helix: 2.04 (0.29), residues: 338 sheet: 1.01 (1.20), residues: 19 loop : 0.61 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS J 258 PHE 0.016 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 273) hydrogen bonds : angle 4.64155 ( 762) covalent geometry : bond 0.00291 ( 5193) covalent geometry : angle 0.53907 ( 7029) *********************** 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 102 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.578 Fit side-chains REVERT: I 260 LYS cc_start: 0.7118 (tttm) cc_final: 0.6918 (ttpp) REVERT: J 99 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6595 (tt0) outliers start: 12 outliers final: 6 residues processed: 96 average time/residue: 1.3306 time to fit residues: 132.6893 Evaluate side-chains 90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 99 GLU 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 40 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.0770 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.163448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144542 restraints weight = 4610.110| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.05 r_work: 0.3617 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5193 Z= 0.177 Angle : 0.595 7.398 7029 Z= 0.303 Chirality : 0.043 0.152 772 Planarity : 0.005 0.043 897 Dihedral : 7.977 79.069 703 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.31 % Favored : 98.53 % Rotamer: Outliers : 3.09 % Allowed : 13.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.34), residues: 612 helix: 1.80 (0.28), residues: 341 sheet: 0.85 (1.22), residues: 19 loop : 0.46 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 273) hydrogen bonds : angle 4.69085 ( 762) covalent geometry : bond 0.00406 ( 5193) covalent geometry : angle 0.59470 ( 7029) *********************** 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 106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.602 Fit side-chains REVERT: H 249 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7107 (mt0) REVERT: I 260 LYS cc_start: 0.7168 (tttm) cc_final: 0.6945 (ttpp) REVERT: J 99 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6602 (tt0) outliers start: 17 outliers final: 5 residues processed: 96 average time/residue: 1.3871 time to fit residues: 138.3986 Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 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 99 GLU Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145573 restraints weight = 4717.122| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.05 r_work: 0.3630 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5193 Z= 0.144 Angle : 0.558 6.860 7029 Z= 0.285 Chirality : 0.042 0.154 772 Planarity : 0.005 0.040 897 Dihedral : 7.546 77.434 703 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.14 % Favored : 98.69 % Rotamer: Outliers : 2.55 % Allowed : 14.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.34), residues: 612 helix: 1.91 (0.28), residues: 341 sheet: 0.62 (1.20), residues: 19 loop : 0.42 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 273) hydrogen bonds : angle 4.58259 ( 762) covalent geometry : bond 0.00328 ( 5193) covalent geometry : angle 0.55845 ( 7029) *********************** 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 104 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.616 Fit side-chains REVERT: I 260 LYS cc_start: 0.7140 (tttm) cc_final: 0.6918 (ttpp) REVERT: J 14 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6961 (tttm) REVERT: J 99 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6603 (tt0) outliers start: 14 outliers final: 6 residues processed: 98 average time/residue: 1.3471 time to fit residues: 137.0465 Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 241 CYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.163658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144905 restraints weight = 4685.382| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.04 r_work: 0.3624 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0794 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= 0.154 Angle : 0.573 7.179 7029 Z= 0.290 Chirality : 0.042 0.158 772 Planarity : 0.005 0.041 897 Dihedral : 7.337 77.851 703 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 3.45 % Allowed : 14.36 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.34), residues: 612 helix: 1.89 (0.28), residues: 341 sheet: 0.51 (1.21), residues: 19 loop : 0.41 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.019 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 273) hydrogen bonds : angle 4.58832 ( 762) covalent geometry : bond 0.00353 ( 5193) covalent geometry : angle 0.57267 ( 7029) *********************** 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 108 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.603 Fit side-chains REVERT: H 249 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7119 (mt0) REVERT: I 242 ARG cc_start: 0.4714 (OUTLIER) cc_final: 0.4424 (mmt180) REVERT: I 261 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7379 (ptmm) REVERT: J 14 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6886 (tttm) REVERT: J 99 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: J 293 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7815 (mptt) outliers start: 19 outliers final: 7 residues processed: 99 average time/residue: 1.2947 time to fit residues: 133.0629 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 : 0.583 ------------------------------------------------------------------------------- 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 I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU 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 43 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.164553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145936 restraints weight = 4713.582| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.05 r_work: 0.3640 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.0795 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= 0.126 Angle : 0.540 6.803 7029 Z= 0.276 Chirality : 0.041 0.156 772 Planarity : 0.005 0.041 897 Dihedral : 7.041 76.521 703 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.36 % Allowed : 15.64 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.34), residues: 612 helix: 2.03 (0.29), residues: 341 sheet: 0.48 (1.20), residues: 19 loop : 0.39 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.002 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 273) hydrogen bonds : angle 4.50140 ( 762) covalent geometry : bond 0.00283 ( 5193) covalent geometry : angle 0.53975 ( 7029) *********************** 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 101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.549 Fit side-chains REVERT: H 249 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7100 (mt0) REVERT: I 261 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7366 (ptmm) REVERT: J 14 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6885 (tttm) REVERT: J 99 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6584 (tt0) outliers start: 13 outliers final: 6 residues processed: 93 average time/residue: 1.4786 time to fit residues: 142.3697 Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU 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 58 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146959 restraints weight = 4722.374| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.07 r_work: 0.3649 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0905 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= 0.114 Angle : 0.518 6.345 7029 Z= 0.265 Chirality : 0.040 0.150 772 Planarity : 0.005 0.041 897 Dihedral : 6.898 75.675 703 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 3.09 % Allowed : 14.91 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.34), residues: 612 helix: 2.16 (0.29), residues: 341 sheet: 0.62 (1.18), residues: 19 loop : 0.41 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.002 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 273) hydrogen bonds : angle 4.40802 ( 762) covalent geometry : bond 0.00253 ( 5193) covalent geometry : angle 0.51818 ( 7029) *********************** 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 107 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.560 Fit side-chains REVERT: I 261 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7343 (ptmm) REVERT: J 99 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6585 (tt0) outliers start: 17 outliers final: 6 residues processed: 101 average time/residue: 1.3015 time to fit residues: 136.4791 Evaluate side-chains 93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 I residue 261 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 231 THR 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 31 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 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 = 0.3955 r_free = 0.3955 target = 0.163675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144742 restraints weight = 4703.356| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.06 r_work: 0.3619 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5193 Z= 0.174 Angle : 0.601 7.612 7029 Z= 0.308 Chirality : 0.044 0.185 772 Planarity : 0.005 0.041 897 Dihedral : 7.015 78.664 702 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.91 % Allowed : 15.27 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.34), residues: 612 helix: 1.87 (0.28), residues: 341 sheet: 0.68 (1.21), residues: 19 loop : 0.38 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.006 0.002 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 273) hydrogen bonds : angle 4.56859 ( 762) covalent geometry : bond 0.00399 ( 5193) covalent geometry : angle 0.60127 ( 7029) *********************** 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 103 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.586 Fit side-chains REVERT: I 261 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7329 (ptmm) REVERT: J 14 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6921 (tttm) REVERT: J 99 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6603 (tt0) REVERT: J 293 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7792 (mptt) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 1.3637 time to fit residues: 132.9343 Evaluate side-chains 96 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 I residue 244 CYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 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 = 0.3965 r_free = 0.3965 target = 0.164373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145869 restraints weight = 4600.055| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.03 r_work: 0.3634 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0850 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= 0.146 Angle : 0.575 8.368 7029 Z= 0.293 Chirality : 0.042 0.153 772 Planarity : 0.005 0.040 897 Dihedral : 6.894 77.211 702 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.36 % Allowed : 15.27 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.34), residues: 612 helix: 1.94 (0.28), residues: 341 sheet: 0.64 (1.21), residues: 19 loop : 0.37 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.007 0.001 HIS J 258 PHE 0.018 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 273) hydrogen bonds : angle 4.51994 ( 762) covalent geometry : bond 0.00332 ( 5193) covalent geometry : angle 0.57508 ( 7029) *********************** 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 100 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.543 Fit side-chains REVERT: I 261 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7298 (ptmm) REVERT: J 14 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6799 (tttm) REVERT: J 99 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: J 293 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7783 (mptt) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 1.3478 time to fit residues: 130.2189 Evaluate side-chains 96 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 I residue 244 CYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5526 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.167115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148258 restraints weight = 4770.601| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.07 r_work: 0.3667 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1083 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= 0.104 Angle : 0.517 7.323 7029 Z= 0.265 Chirality : 0.040 0.148 772 Planarity : 0.005 0.043 897 Dihedral : 6.647 74.422 702 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.34), residues: 612 helix: 2.24 (0.29), residues: 339 sheet: 0.74 (1.14), residues: 19 loop : 0.38 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.001 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.002 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 273) hydrogen bonds : angle 4.34253 ( 762) covalent geometry : bond 0.00228 ( 5193) covalent geometry : angle 0.51704 ( 7029) ********************** 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 102 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.614 Fit side-chains REVERT: H 249 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: I 260 LYS cc_start: 0.7039 (tttm) cc_final: 0.6824 (ttpp) REVERT: J 14 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6741 (tttm) REVERT: J 99 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6537 (tt0) outliers start: 11 outliers final: 6 residues processed: 97 average time/residue: 1.3279 time to fit residues: 133.6954 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 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 244 CYS Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 231 THR 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 8 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.166703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147775 restraints weight = 4791.877| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.08 r_work: 0.3658 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1153 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 : 0.534 7.652 7029 Z= 0.274 Chirality : 0.041 0.169 772 Planarity : 0.005 0.042 897 Dihedral : 6.639 74.859 702 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 1.64 % Allowed : 17.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.34), residues: 612 helix: 2.20 (0.29), residues: 341 sheet: 0.84 (1.16), residues: 19 loop : 0.35 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.002 PHE J 252 TYR 0.017 0.002 TYR H 287 ARG 0.004 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 273) hydrogen bonds : angle 4.34750 ( 762) covalent geometry : bond 0.00247 ( 5193) covalent geometry : angle 0.53415 ( 7029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4920.48 seconds wall clock time: 85 minutes 35.74 seconds (5135.74 seconds total)