Starting phenix.real_space_refine on Thu Jul 2 01:34:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6y_17511/07_2026/8p6y_17511.cif" } resolution = 1.9 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3279 2.51 5 N 869 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5266 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 1.27, per 1000 atoms: 0.24 Number of scatterers: 5266 At special positions: 0 Unit cell: (84.7875, 94.7625, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 3 15.00 Mg 1 11.99 O 1082 8.00 N 869 7.00 C 3279 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: 0.41 Conformation dependent library (CDL) restraints added in 139.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 63.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.883A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.546A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.983A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.703A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.622A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.571A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.613A 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 200 Processing helix chain 'I' and resid 201 through 206 removed outlier: 4.519A pdb=" N TYR I 204 " --> pdb=" O THR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.743A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 removed outlier: 3.539A pdb=" N GLU I 240 " --> pdb=" O MET I 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 237 through 240' Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.435A 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: 3.886A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 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: 3.824A 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 13 through 19 removed outlier: 7.149A pdb=" N LEU J 15 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ARG J 30 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.974A 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 134 274 hydrogen bonds defined for protein. 759 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: 0.68 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1669 1.36 - 1.50: 1384 1.50 - 1.64: 2120 1.64 - 1.78: 7 1.78 - 1.91: 50 Bond restraints: 5230 Sorted by residual: bond pdb=" C6 AGS J 401 " pdb=" N6 AGS J 401 " ideal model delta sigma weight residual 1.335 1.457 -0.122 1.00e-02 1.00e+04 1.48e+02 bond pdb=" C1' AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 1.459 1.319 0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 bond pdb=" O3B AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sigma weight residual 1.559 1.656 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " ideal model delta sigma weight residual 1.386 1.338 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 5225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6949 1.77 - 3.53: 105 3.53 - 5.30: 22 5.30 - 7.06: 5 7.06 - 8.83: 4 Bond angle restraints: 7085 Sorted by residual: angle pdb=" N1 AGS J 401 " pdb=" C2 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 128.80 120.14 8.66 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " ideal model delta sigma weight residual 103.67 107.94 -4.27 4.26e-01 5.51e+00 1.01e+02 angle pdb=" C5 AGS J 401 " pdb=" C4 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 126.80 119.81 6.99 7.41e-01 1.82e+00 8.90e+01 angle pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 114.03 108.21 5.82 6.99e-01 2.05e+00 6.93e+01 angle pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 110.73 108.03 2.70 4.52e-01 4.89e+00 3.57e+01 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 2816 19.94 - 39.88: 254 39.88 - 59.81: 68 59.81 - 79.75: 10 79.75 - 99.69: 8 Dihedral angle restraints: 3156 sinusoidal: 1309 harmonic: 1847 Sorted by residual: dihedral pdb=" O1B AGS J 401 " pdb=" O3B AGS J 401 " pdb=" PB AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sinusoidal sigma weight residual 68.91 168.60 -99.69 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" CB GLU I 145 " pdb=" CG GLU I 145 " pdb=" CD GLU I 145 " pdb=" OE1 GLU I 145 " ideal model delta sinusoidal sigma weight residual 0.00 90.26 -90.26 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 3153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 613 0.047 - 0.094: 131 0.094 - 0.142: 34 0.142 - 0.189: 1 0.189 - 0.236: 2 Chirality restraints: 781 Sorted by residual: chirality pdb=" C1' AGS J 401 " pdb=" C2' AGS J 401 " pdb=" N9 AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False 2.41 2.17 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2' AGS J 401 " pdb=" C1' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" O2' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.67 -2.87 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C4' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" C5' AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.63 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 778 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 66 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" CD GLU I 66 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU I 66 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU I 66 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 183 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO I 184 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO J 140 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 186 2.70 - 3.25: 5265 3.25 - 3.80: 9244 3.80 - 4.35: 12178 4.35 - 4.90: 19355 Nonbonded interactions: 46228 Sorted by model distance: nonbonded pdb="MG MG J 402 " pdb=" O HOH J 551 " model vdw 2.148 2.170 nonbonded pdb=" O ARG I 242 " pdb=" NH1 ARG I 242 " model vdw 2.203 3.120 nonbonded pdb=" O HOH J 535 " pdb=" O HOH J 561 " model vdw 2.246 3.040 nonbonded pdb=" O HOH I 402 " pdb=" O HOH I 467 " model vdw 2.255 3.040 nonbonded pdb=" O HOH J 505 " pdb=" O HOH J 539 " model vdw 2.260 3.040 ... (remaining 46223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.880 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.005 0.140 5230 Z= 0.336 Angle : 0.600 8.826 7085 Z= 0.400 Chirality : 0.042 0.236 781 Planarity : 0.004 0.036 902 Dihedral : 16.817 99.688 1960 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.36 % Allowed : 15.34 % Favored : 84.30 % 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 are not related in a simple way. whole: 1.99 (0.34), residues: 618 helix: 2.21 (0.29), residues: 331 sheet: -0.61 (1.27), residues: 19 loop : 0.43 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.016 0.001 TYR I 91 PHE 0.013 0.002 PHE I 110 TRP 0.006 0.001 TRP I 11 HIS 0.009 0.001 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.34 ( 5230) covalent geometry : angle 0.60002 / 0.40 ( 7085) hydrogen bonds : bond 0.13824 / 8.65 ( 274) hydrogen bonds : angle 5.80312 / 4.15 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.209 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.6864 time to fit residues: 63.8076 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.158356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134206 restraints weight = 4530.812| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 0.82 r_work: 0.3418 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5230 Z= 0.141 Angle : 0.577 8.492 7085 Z= 0.296 Chirality : 0.042 0.149 781 Planarity : 0.005 0.034 902 Dihedral : 6.786 95.136 701 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 14.08 % Favored : 84.84 % 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 are not related in a simple way. whole: 2.04 (0.34), residues: 618 helix: 2.29 (0.28), residues: 338 sheet: -0.30 (1.00), residues: 25 loop : 0.32 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 61 TYR 0.017 0.002 TYR I 91 PHE 0.013 0.002 PHE J 295 TRP 0.008 0.001 TRP J 132 HIS 0.010 0.002 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 5230) covalent geometry : angle 0.57741 / 0.30 ( 7085) hydrogen bonds : bond 0.05583 / 3.49 ( 274) hydrogen bonds : angle 4.67733 / 3.31 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.195 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.7423 time to fit residues: 73.3465 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN I 124 GLN J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131857 restraints weight = 4439.446| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.82 r_work: 0.3384 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5230 Z= 0.272 Angle : 0.770 8.695 7085 Z= 0.396 Chirality : 0.049 0.202 781 Planarity : 0.006 0.043 902 Dihedral : 6.980 87.335 698 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.81 % Allowed : 12.82 % Favored : 85.38 % 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 are not related in a simple way. whole: 1.51 (0.33), residues: 618 helix: 1.82 (0.27), residues: 338 sheet: -0.65 (0.98), residues: 25 loop : 0.14 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 61 TYR 0.021 0.003 TYR I 91 PHE 0.021 0.003 PHE I 13 TRP 0.013 0.003 TRP J 132 HIS 0.013 0.003 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 ( 5230) covalent geometry : angle 0.77041 / 0.40 ( 7085) hydrogen bonds : bond 0.07111 / 4.49 ( 274) hydrogen bonds : angle 4.99518 / 3.54 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.212 Fit side-chains REVERT: I 18 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: J 52 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6734 (mmtm) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.7326 time to fit residues: 67.3148 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN I 124 GLN J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132103 restraints weight = 4472.253| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 0.82 r_work: 0.3387 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5230 Z= 0.231 Angle : 0.722 8.263 7085 Z= 0.370 Chirality : 0.047 0.184 781 Planarity : 0.006 0.039 902 Dihedral : 6.920 86.927 698 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.81 % Allowed : 13.54 % Favored : 84.66 % 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 are not related in a simple way. whole: 1.47 (0.33), residues: 618 helix: 1.79 (0.27), residues: 338 sheet: -0.77 (1.19), residues: 19 loop : 0.12 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 30 TYR 0.019 0.002 TYR I 2 PHE 0.019 0.003 PHE I 13 TRP 0.013 0.002 TRP J 132 HIS 0.012 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 ( 5230) covalent geometry : angle 0.72152 / 0.37 ( 7085) hydrogen bonds : bond 0.06659 / 4.19 ( 274) hydrogen bonds : angle 4.90209 / 3.47 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.224 Fit side-chains REVERT: J 52 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6529 (mmtm) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.7077 time to fit residues: 65.7731 Evaluate side-chains 91 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.0060 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.158807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134497 restraints weight = 4555.618| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 0.83 r_work: 0.3421 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5230 Z= 0.123 Angle : 0.571 8.977 7085 Z= 0.290 Chirality : 0.042 0.140 781 Planarity : 0.004 0.036 902 Dihedral : 6.630 87.241 698 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 14.62 % Favored : 84.30 % 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 are not related in a simple way. whole: 1.88 (0.34), residues: 618 helix: 2.22 (0.28), residues: 338 sheet: -0.30 (0.97), residues: 25 loop : 0.15 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 61 TYR 0.015 0.001 TYR I 91 PHE 0.015 0.002 PHE I 30 TRP 0.007 0.001 TRP J 132 HIS 0.010 0.001 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 5230) covalent geometry : angle 0.57091 / 0.29 ( 7085) hydrogen bonds : bond 0.05141 / 3.21 ( 274) hydrogen bonds : angle 4.54007 / 3.21 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.222 Fit side-chains REVERT: I 18 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7987 (tt0) outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 0.7420 time to fit residues: 69.6471 Evaluate side-chains 90 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.0270 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.160237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136035 restraints weight = 4565.196| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 0.83 r_work: 0.3440 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5230 Z= 0.109 Angle : 0.531 8.849 7085 Z= 0.269 Chirality : 0.041 0.136 781 Planarity : 0.004 0.035 902 Dihedral : 6.421 84.693 698 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.26 % Allowed : 14.44 % Favored : 84.30 % 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 are not related in a simple way. whole: 2.06 (0.34), residues: 618 helix: 2.32 (0.28), residues: 344 sheet: -0.08 (0.96), residues: 25 loop : 0.23 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 61 TYR 0.014 0.001 TYR I 91 PHE 0.013 0.002 PHE I 30 TRP 0.005 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 5230) covalent geometry : angle 0.53114 / 0.27 ( 7085) hydrogen bonds : bond 0.04598 / 2.86 ( 274) hydrogen bonds : angle 4.34234 / 3.06 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.203 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.7005 time to fit residues: 67.1142 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 24 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133211 restraints weight = 4484.254| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 0.83 r_work: 0.3404 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5230 Z= 0.179 Angle : 0.649 9.579 7085 Z= 0.330 Chirality : 0.044 0.154 781 Planarity : 0.005 0.036 902 Dihedral : 6.650 83.155 698 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.81 % Favored : 99.03 % Rotamer: Outliers : 1.44 % Allowed : 14.80 % Favored : 83.75 % 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 are not related in a simple way. whole: 1.84 (0.34), residues: 618 helix: 2.15 (0.28), residues: 338 sheet: -0.39 (0.96), residues: 25 loop : 0.19 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 188 TYR 0.019 0.002 TYR I 91 PHE 0.016 0.002 PHE I 13 TRP 0.010 0.002 TRP J 132 HIS 0.011 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 5230) covalent geometry : angle 0.64905 / 0.33 ( 7085) hydrogen bonds : bond 0.05902 / 3.72 ( 274) hydrogen bonds : angle 4.64218 / 3.28 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.225 Fit side-chains REVERT: J 52 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6293 (mmtt) outliers start: 8 outliers final: 6 residues processed: 94 average time/residue: 0.7243 time to fit residues: 70.1865 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 36 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135315 restraints weight = 4475.466| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 0.81 r_work: 0.3432 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5230 Z= 0.122 Angle : 0.569 10.919 7085 Z= 0.288 Chirality : 0.041 0.139 781 Planarity : 0.004 0.034 902 Dihedral : 6.473 83.656 698 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.26 % Allowed : 14.98 % Favored : 83.75 % 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 are not related in a simple way. whole: 2.05 (0.34), residues: 618 helix: 2.36 (0.28), residues: 338 sheet: -0.20 (0.94), residues: 25 loop : 0.22 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 188 TYR 0.015 0.001 TYR I 91 PHE 0.014 0.002 PHE I 30 TRP 0.006 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 5230) covalent geometry : angle 0.56926 / 0.29 ( 7085) hydrogen bonds : bond 0.04908 / 3.07 ( 274) hydrogen bonds : angle 4.41832 / 3.11 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.137 Fit side-chains REVERT: I 18 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: J 52 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6324 (mmtt) outliers start: 7 outliers final: 3 residues processed: 94 average time/residue: 0.7612 time to fit residues: 73.6311 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134958 restraints weight = 4545.236| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 0.82 r_work: 0.3426 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5230 Z= 0.127 Angle : 0.580 10.455 7085 Z= 0.294 Chirality : 0.042 0.137 781 Planarity : 0.004 0.034 902 Dihedral : 6.465 82.419 698 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 1.26 % Allowed : 14.80 % Favored : 83.94 % 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 are not related in a simple way. whole: 2.08 (0.34), residues: 618 helix: 2.37 (0.28), residues: 337 sheet: -0.20 (0.94), residues: 25 loop : 0.27 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 188 TYR 0.015 0.001 TYR I 91 PHE 0.014 0.002 PHE I 30 TRP 0.006 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 5230) covalent geometry : angle 0.57968 / 0.29 ( 7085) hydrogen bonds : bond 0.05006 / 3.14 ( 274) hydrogen bonds : angle 4.42444 / 3.11 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.193 Fit side-chains REVERT: I 18 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: J 52 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6377 (mmtt) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.8501 time to fit residues: 80.4213 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 0.2980 chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.0050 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138182 restraints weight = 4613.862| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 0.82 r_work: 0.3471 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5230 Z= 0.104 Angle : 0.532 10.082 7085 Z= 0.268 Chirality : 0.040 0.149 781 Planarity : 0.004 0.034 902 Dihedral : 6.215 80.645 698 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 0.90 % Allowed : 15.34 % Favored : 83.75 % 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 are not related in a simple way. whole: 2.20 (0.34), residues: 618 helix: 2.39 (0.28), residues: 344 sheet: 0.01 (0.93), residues: 25 loop : 0.35 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 188 TYR 0.014 0.001 TYR I 60 PHE 0.013 0.001 PHE I 110 TRP 0.004 0.001 TRP I 11 HIS 0.010 0.001 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 5230) covalent geometry : angle 0.53193 / 0.27 ( 7085) hydrogen bonds : bond 0.04100 / 2.54 ( 274) hydrogen bonds : angle 4.20962 / 2.94 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.211 Fit side-chains REVERT: J 52 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6322 (mmtt) outliers start: 5 outliers final: 1 residues processed: 98 average time/residue: 0.8013 time to fit residues: 80.9899 Evaluate side-chains 87 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.159673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135240 restraints weight = 4567.839| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 0.83 r_work: 0.3431 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5230 Z= 0.131 Angle : 0.585 9.951 7085 Z= 0.297 Chirality : 0.042 0.198 781 Planarity : 0.004 0.034 902 Dihedral : 6.389 79.642 698 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.36 % Allowed : 16.61 % Favored : 83.03 % 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 are not related in a simple way. whole: 2.19 (0.34), residues: 618 helix: 2.43 (0.28), residues: 338 sheet: -0.13 (0.95), residues: 25 loop : 0.34 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 268 TYR 0.016 0.002 TYR I 91 PHE 0.014 0.002 PHE I 110 TRP 0.008 0.001 TRP J 132 HIS 0.009 0.002 HIS J 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 5230) covalent geometry : angle 0.58543 / 0.30 ( 7085) hydrogen bonds : bond 0.04963 / 3.12 ( 274) hydrogen bonds : angle 4.36065 / 3.07 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3001.48 seconds wall clock time: 51 minutes 48.47 seconds (3108.47 seconds total)