Starting phenix.real_space_refine on Wed Jul 1 22:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws7_37800/07_2026/8ws7_37800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws7_37800/07_2026/8ws7_37800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2026/8ws7_37800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2026/8ws7_37800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2026/8ws7_37800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2026/8ws7_37800.map" } resolution = 3.26 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= 0.001 sd= 0.015 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 P 54 5.49 5 S 3 5.16 5 C 1934 2.51 5 N 604 2.21 5 O 738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 3333 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2207 Classifications: {'peptide': 279} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 251} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 360 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 627 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 23} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 0.99, per 1000 atoms: 0.30 Number of scatterers: 3333 At special positions: 0 Unit cell: (54.78, 77.88, 91.08, 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) S 3 16.00 P 54 15.00 O 738 8.00 N 604 7.00 C 1934 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: 0.32 Conformation dependent library (CDL) restraints added in 80.7 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 38.0% alpha, 7.9% beta 9 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.087A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.654A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 158 removed outlier: 3.582A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.534A pdb=" N ARG A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.559A pdb=" N LEU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.684A pdb=" N ILE A 198 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 296 " --> pdb=" O MET A 307 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 774 1.33 - 1.45: 971 1.45 - 1.57: 1670 1.57 - 1.69: 105 1.69 - 1.81: 4 Bond restraints: 3524 Sorted by residual: bond pdb=" CA LYS A 273 " pdb=" C LYS A 273 " ideal model delta sigma weight residual 1.522 1.561 -0.039 1.06e-02 8.90e+03 1.33e+01 bond pdb=" C3' DA C -10 " pdb=" C2' DA C -10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT C -7 " pdb=" C2' DT C -7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.87e+00 bond pdb=" CA ARG A 70 " pdb=" C ARG A 70 " ideal model delta sigma weight residual 1.519 1.547 -0.028 1.01e-02 9.80e+03 7.89e+00 ... (remaining 3519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 4741 1.45 - 2.90: 239 2.90 - 4.35: 29 4.35 - 5.80: 4 5.80 - 7.25: 2 Bond angle restraints: 5015 Sorted by residual: angle pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sigma weight residual 117.70 122.74 -5.04 1.20e+00 6.94e-01 1.76e+01 angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 ... (remaining 5010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 1926 34.05 - 68.10: 172 68.10 - 102.14: 17 102.14 - 136.19: 0 136.19 - 170.24: 2 Dihedral angle restraints: 2117 sinusoidal: 1322 harmonic: 795 Sorted by residual: dihedral pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sinusoidal sigma weight residual 200.00 58.25 141.75 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 61.76 170.24 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CA TRP A 318 " pdb=" C TRP A 318 " pdb=" N ARG A 319 " pdb=" CA ARG A 319 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 2114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 462 0.052 - 0.103: 80 0.103 - 0.155: 26 0.155 - 0.206: 1 0.206 - 0.258: 2 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA LEU A 72 " pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CB LEU A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 198 " pdb=" N ILE A 198 " pdb=" C ILE A 198 " pdb=" CB ILE A 198 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS A 273 " pdb=" N LYS A 273 " pdb=" C LYS A 273 " pdb=" CB LYS A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 568 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 70 " -0.040 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 71 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 69 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER A 69 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 69 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 70 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 75 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 76 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.025 5.00e-02 4.00e+02 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 809 2.80 - 3.32: 2904 3.32 - 3.85: 5913 3.85 - 4.37: 7050 4.37 - 4.90: 10629 Nonbonded interactions: 27305 Sorted by model distance: nonbonded pdb=" NE2 GLN A 127 " pdb=" O4 DT D -2 " model vdw 2.272 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" O6 G B -16 " model vdw 2.314 3.120 nonbonded pdb=" O2' C B -6 " pdb=" OP2 C B -5 " model vdw 2.334 3.040 nonbonded pdb=" O6 DG C 5 " pdb=" N4 DC D -6 " model vdw 2.371 3.120 nonbonded pdb=" N6 DA C -10 " pdb=" O4 U B 10 " model vdw 2.425 3.120 ... (remaining 27300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.830 Find NCS groups from input model: 0.000 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 0.039 3524 Z= 0.340 Angle : 0.696 7.250 5015 Z= 0.515 Chirality : 0.046 0.258 571 Planarity : 0.006 0.062 450 Dihedral : 21.449 170.241 1609 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.86 % Allowed : 1.72 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.50), residues: 275 helix: -1.23 (0.51), residues: 98 sheet: 0.58 (1.11), residues: 26 loop : -0.78 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.006 0.001 TYR A 201 PHE 0.009 0.001 PHE A 334 TRP 0.013 0.002 TRP A 318 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.34 ( 3524) covalent geometry : angle 0.69591 / 0.51 ( 5015) hydrogen bonds : bond 0.25870 / 17.40 ( 94) hydrogen bonds : angle 9.73398 / 6.85 ( 247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.091 Fit side-chains REVERT: A 74 GLU cc_start: 0.6450 (mp0) cc_final: 0.6114 (mp0) REVERT: A 302 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7762 (mtpp) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.1443 time to fit residues: 4.9288 Evaluate side-chains 26 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126403 restraints weight = 4833.799| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.31 r_work: 0.3492 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3524 Z= 0.222 Angle : 0.682 8.824 5015 Z= 0.381 Chirality : 0.047 0.196 571 Planarity : 0.007 0.045 450 Dihedral : 24.078 172.476 1055 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.86 % Allowed : 7.76 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.48), residues: 275 helix: -0.96 (0.48), residues: 100 sheet: 0.00 (0.97), residues: 33 loop : -0.75 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 111 TYR 0.008 0.002 TYR A 201 PHE 0.020 0.002 PHE A 350 TRP 0.016 0.002 TRP A 112 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 ( 3524) covalent geometry : angle 0.68182 / 0.38 ( 5015) hydrogen bonds : bond 0.06998 / 4.65 ( 94) hydrogen bonds : angle 5.74167 / 3.99 ( 247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.101 Fit side-chains REVERT: A 74 GLU cc_start: 0.7079 (mp0) cc_final: 0.6645 (mp0) REVERT: A 155 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6841 (ttp-170) REVERT: A 302 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8269 (mtpp) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.1473 time to fit residues: 5.5554 Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125545 restraints weight = 4962.924| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.37 r_work: 0.3486 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3524 Z= 0.217 Angle : 0.660 7.559 5015 Z= 0.369 Chirality : 0.046 0.174 571 Planarity : 0.006 0.044 450 Dihedral : 23.960 174.058 1055 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 11.64 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.47), residues: 275 helix: -0.75 (0.49), residues: 102 sheet: -0.58 (1.01), residues: 28 loop : -0.70 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 314 TYR 0.007 0.002 TYR A 201 PHE 0.018 0.003 PHE A 350 TRP 0.018 0.002 TRP A 112 HIS 0.004 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 ( 3524) covalent geometry : angle 0.66044 / 0.37 ( 5015) hydrogen bonds : bond 0.06014 / 4.15 ( 94) hydrogen bonds : angle 5.23641 / 3.67 ( 247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.091 Fit side-chains REVERT: A 74 GLU cc_start: 0.7160 (mp0) cc_final: 0.6697 (mp0) REVERT: A 155 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6852 (ttp-170) REVERT: A 302 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8315 (mtpp) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.1243 time to fit residues: 4.8335 Evaluate side-chains 32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.0470 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127045 restraints weight = 4841.224| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.33 r_work: 0.3517 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3524 Z= 0.163 Angle : 0.597 6.955 5015 Z= 0.337 Chirality : 0.043 0.175 571 Planarity : 0.005 0.043 450 Dihedral : 23.816 174.859 1055 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.31 % Allowed : 10.78 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.48), residues: 275 helix: -0.32 (0.50), residues: 102 sheet: -0.69 (0.89), residues: 33 loop : -0.66 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.008 0.001 TYR A 201 PHE 0.013 0.002 PHE A 350 TRP 0.013 0.002 TRP A 112 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 3524) covalent geometry : angle 0.59725 / 0.34 ( 5015) hydrogen bonds : bond 0.05332 / 3.62 ( 94) hydrogen bonds : angle 4.89590 / 3.43 ( 247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.054 Fit side-chains REVERT: A 74 GLU cc_start: 0.7135 (mp0) cc_final: 0.6657 (mp0) REVERT: A 302 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8249 (mtpp) outliers start: 10 outliers final: 4 residues processed: 34 average time/residue: 0.0793 time to fit residues: 3.0509 Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125952 restraints weight = 4843.305| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.34 r_work: 0.3478 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3524 Z= 0.195 Angle : 0.629 10.161 5015 Z= 0.348 Chirality : 0.045 0.171 571 Planarity : 0.006 0.043 450 Dihedral : 23.666 174.952 1051 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.88 % Allowed : 12.50 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.48), residues: 275 helix: -0.28 (0.50), residues: 102 sheet: -0.97 (0.98), residues: 28 loop : -0.65 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.007 0.002 TYR A 201 PHE 0.017 0.003 PHE A 350 TRP 0.015 0.002 TRP A 112 HIS 0.004 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 ( 3524) covalent geometry : angle 0.62943 / 0.35 ( 5015) hydrogen bonds : bond 0.05263 / 3.66 ( 94) hydrogen bonds : angle 4.96671 / 3.46 ( 247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.083 Fit side-chains REVERT: A 74 GLU cc_start: 0.7205 (mp0) cc_final: 0.6753 (mp0) REVERT: A 302 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8304 (mtpp) REVERT: A 332 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6456 (mp) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.0969 time to fit residues: 3.7458 Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 3 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 11 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126173 restraints weight = 4877.948| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.31 r_work: 0.3503 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3524 Z= 0.149 Angle : 0.578 9.073 5015 Z= 0.322 Chirality : 0.042 0.171 571 Planarity : 0.005 0.042 450 Dihedral : 23.620 175.665 1051 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.88 % Allowed : 15.09 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.48), residues: 275 helix: 0.03 (0.51), residues: 102 sheet: -0.79 (0.87), residues: 33 loop : -0.68 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 134 TYR 0.008 0.001 TYR A 201 PHE 0.013 0.002 PHE A 350 TRP 0.014 0.002 TRP A 318 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 ( 3524) covalent geometry : angle 0.57756 / 0.32 ( 5015) hydrogen bonds : bond 0.04851 / 3.33 ( 94) hydrogen bonds : angle 4.86813 / 3.38 ( 247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.085 Fit side-chains REVERT: A 74 GLU cc_start: 0.7119 (mp0) cc_final: 0.6660 (mp0) REVERT: A 302 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8253 (mtpp) outliers start: 9 outliers final: 6 residues processed: 33 average time/residue: 0.1054 time to fit residues: 3.9562 Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.0010 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124849 restraints weight = 4900.698| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.37 r_work: 0.3468 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3524 Z= 0.222 Angle : 0.633 7.117 5015 Z= 0.349 Chirality : 0.046 0.168 571 Planarity : 0.006 0.045 450 Dihedral : 23.670 175.374 1051 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.31 % Allowed : 15.95 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.48), residues: 275 helix: -0.16 (0.50), residues: 102 sheet: -1.18 (0.97), residues: 28 loop : -0.65 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 271 TYR 0.008 0.002 TYR A 89 PHE 0.018 0.003 PHE A 350 TRP 0.017 0.002 TRP A 112 HIS 0.005 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 ( 3524) covalent geometry : angle 0.63270 / 0.35 ( 5015) hydrogen bonds : bond 0.05263 / 3.67 ( 94) hydrogen bonds : angle 4.97991 / 3.49 ( 247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.077 Fit side-chains REVERT: A 74 GLU cc_start: 0.7209 (mp0) cc_final: 0.6703 (mp0) REVERT: A 190 GLU cc_start: 0.6505 (mp0) cc_final: 0.6201 (mt-10) REVERT: A 302 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8339 (mtpp) REVERT: A 330 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 332 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6410 (mt) outliers start: 10 outliers final: 8 residues processed: 37 average time/residue: 0.0690 time to fit residues: 2.9809 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125901 restraints weight = 4890.464| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.34 r_work: 0.3496 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3524 Z= 0.172 Angle : 0.592 6.722 5015 Z= 0.329 Chirality : 0.043 0.168 571 Planarity : 0.006 0.043 450 Dihedral : 23.685 175.917 1051 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.60 % Allowed : 14.66 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.48), residues: 275 helix: 0.03 (0.50), residues: 102 sheet: -0.94 (0.87), residues: 33 loop : -0.70 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 134 TYR 0.008 0.001 TYR A 201 PHE 0.013 0.002 PHE A 350 TRP 0.015 0.002 TRP A 112 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 3524) covalent geometry : angle 0.59190 / 0.33 ( 5015) hydrogen bonds : bond 0.04942 / 3.41 ( 94) hydrogen bonds : angle 4.87692 / 3.42 ( 247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.053 Fit side-chains REVERT: A 74 GLU cc_start: 0.7166 (mp0) cc_final: 0.6659 (mp0) REVERT: A 190 GLU cc_start: 0.6493 (mp0) cc_final: 0.6192 (mp0) REVERT: A 302 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8316 (mtpp) REVERT: A 330 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 332 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6500 (mt) outliers start: 13 outliers final: 12 residues processed: 37 average time/residue: 0.0670 time to fit residues: 2.8773 Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 17 optimal weight: 0.0570 chunk 24 optimal weight: 0.0770 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127949 restraints weight = 4873.870| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.34 r_work: 0.3521 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3524 Z= 0.127 Angle : 0.549 6.864 5015 Z= 0.307 Chirality : 0.040 0.171 571 Planarity : 0.005 0.043 450 Dihedral : 23.617 177.145 1051 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.31 % Allowed : 16.81 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.49), residues: 275 helix: 0.39 (0.52), residues: 104 sheet: -0.84 (0.87), residues: 33 loop : -0.62 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.010 0.001 PHE A 350 TRP 0.015 0.002 TRP A 318 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 3524) covalent geometry : angle 0.54941 / 0.31 ( 5015) hydrogen bonds : bond 0.04470 / 3.09 ( 94) hydrogen bonds : angle 4.66200 / 3.26 ( 247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.059 Fit side-chains REVERT: A 74 GLU cc_start: 0.7071 (mp0) cc_final: 0.6631 (mp0) REVERT: A 190 GLU cc_start: 0.6415 (mp0) cc_final: 0.6124 (mt-10) REVERT: A 280 LEU cc_start: 0.6533 (mm) cc_final: 0.6322 (tp) REVERT: A 302 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8212 (mtpp) REVERT: A 330 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6996 (tm-30) outliers start: 10 outliers final: 7 residues processed: 36 average time/residue: 0.0847 time to fit residues: 3.4815 Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.0030 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127203 restraints weight = 4910.626| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.32 r_work: 0.3505 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3524 Z= 0.158 Angle : 0.567 7.224 5015 Z= 0.315 Chirality : 0.041 0.171 571 Planarity : 0.006 0.043 450 Dihedral : 23.618 176.913 1051 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.74 % Allowed : 16.38 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.49), residues: 275 helix: 0.37 (0.51), residues: 104 sheet: -0.86 (0.87), residues: 33 loop : -0.61 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.013 0.002 PHE A 350 TRP 0.014 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 3524) covalent geometry : angle 0.56682 / 0.32 ( 5015) hydrogen bonds : bond 0.04550 / 3.16 ( 94) hydrogen bonds : angle 4.63951 / 3.27 ( 247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.055 Fit side-chains REVERT: A 74 GLU cc_start: 0.7097 (mp0) cc_final: 0.6645 (mp0) REVERT: A 111 ARG cc_start: 0.7156 (ptm-80) cc_final: 0.6674 (ptt90) REVERT: A 302 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8255 (mtpp) REVERT: A 330 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6997 (tm-30) outliers start: 11 outliers final: 9 residues processed: 38 average time/residue: 0.1200 time to fit residues: 5.1593 Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.0030 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127769 restraints weight = 4927.699| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.31 r_work: 0.3509 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3524 Z= 0.136 Angle : 0.547 8.713 5015 Z= 0.305 Chirality : 0.040 0.172 571 Planarity : 0.005 0.042 450 Dihedral : 23.617 177.477 1051 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.88 % Allowed : 16.81 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.50), residues: 275 helix: 0.49 (0.52), residues: 104 sheet: -0.79 (0.86), residues: 33 loop : -0.57 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 134 TYR 0.007 0.001 TYR A 201 PHE 0.012 0.002 PHE A 350 TRP 0.014 0.002 TRP A 270 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 3524) covalent geometry : angle 0.54702 / 0.30 ( 5015) hydrogen bonds : bond 0.04362 / 3.01 ( 94) hydrogen bonds : angle 4.53669 / 3.21 ( 247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 895.31 seconds wall clock time: 16 minutes 1.20 seconds (961.20 seconds total)