Starting phenix.real_space_refine on Tue Feb 3 20:59:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfp_61435/02_2026/9jfp_61435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfp_61435/02_2026/9jfp_61435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jfp_61435/02_2026/9jfp_61435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfp_61435/02_2026/9jfp_61435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jfp_61435/02_2026/9jfp_61435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfp_61435/02_2026/9jfp_61435.map" } resolution = 2.96 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= 0.061 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 164 5.49 5 S 15 5.16 5 C 3743 2.51 5 N 1273 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6921 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 329 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2875 Classifications: {'RNA': 134} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 67, 'rna3p_pyr': 52} Link IDs: {'rna2p': 15, 'rna3p': 118} Chain breaks: 2 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3432 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 1 Time building chain proxies: 1.73, per 1000 atoms: 0.25 Number of scatterers: 6921 At special positions: 0 Unit cell: (103.726, 94.4496, 118.062, 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 15 16.00 P 164 15.00 O 1726 8.00 N 1273 7.00 C 3743 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: 0.79 Conformation dependent library (CDL) restraints added in 120.2 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 45.5% alpha, 10.9% beta 57 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.607A pdb=" N ARG A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.664A pdb=" N LYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.897A pdb=" N ASP A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 339 through 375 removed outlier: 3.666A pdb=" N ILE A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 415 removed outlier: 3.928A pdb=" N PHE A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.244A pdb=" N THR A 206 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS A 174 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 removed outlier: 7.331A pdb=" N TYR A 268 " --> pdb=" O ILE A 259 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.00 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: 1377 1.33 - 1.45: 2499 1.45 - 1.57: 3180 1.57 - 1.69: 322 1.69 - 1.81: 26 Bond restraints: 7404 Sorted by residual: bond pdb=" O3' C F 21 " pdb=" P A F 22 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.02e+01 bond pdb=" O5' G F 77 " pdb=" C5' G F 77 " ideal model delta sigma weight residual 1.424 1.446 -0.022 1.50e-02 4.44e+03 2.25e+00 bond pdb=" O3' G F 77 " pdb=" P A F 78 " ideal model delta sigma weight residual 1.607 1.627 -0.020 1.50e-02 4.44e+03 1.86e+00 bond pdb=" C3' G F 77 " pdb=" O3' G F 77 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.77e+00 bond pdb=" C3' A F 22 " pdb=" O3' A F 22 " ideal model delta sigma weight residual 1.417 1.436 -0.019 1.50e-02 4.44e+03 1.63e+00 ... (remaining 7399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10572 1.77 - 3.53: 185 3.53 - 5.30: 22 5.30 - 7.06: 3 7.06 - 8.83: 3 Bond angle restraints: 10785 Sorted by residual: angle pdb=" C4' G F 77 " pdb=" C3' G F 77 " pdb=" O3' G F 77 " ideal model delta sigma weight residual 109.40 118.23 -8.83 1.50e+00 4.44e-01 3.46e+01 angle pdb=" O3' C F 76 " pdb=" C3' C F 76 " pdb=" C2' C F 76 " ideal model delta sigma weight residual 109.50 118.06 -8.56 1.50e+00 4.44e-01 3.25e+01 angle pdb=" O4' U F 23 " pdb=" C1' U F 23 " pdb=" C2' U F 23 " ideal model delta sigma weight residual 105.80 110.08 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" C GLY A 60 " pdb=" N ASP A 61 " pdb=" CA ASP A 61 " ideal model delta sigma weight residual 120.94 127.89 -6.95 1.90e+00 2.77e-01 1.34e+01 angle pdb=" C4' A F 22 " pdb=" C3' A F 22 " pdb=" C2' A F 22 " ideal model delta sigma weight residual 102.60 99.00 3.60 1.00e+00 1.00e+00 1.29e+01 ... (remaining 10780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 3992 35.53 - 71.07: 514 71.07 - 106.60: 49 106.60 - 142.14: 3 142.14 - 177.67: 4 Dihedral angle restraints: 4562 sinusoidal: 3297 harmonic: 1265 Sorted by residual: dihedral pdb=" O4' C F 88 " pdb=" C1' C F 88 " pdb=" N1 C F 88 " pdb=" C2 C F 88 " ideal model delta sinusoidal sigma weight residual -128.00 49.67 -177.67 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U F 23 " pdb=" C2' U F 23 " pdb=" C1' U F 23 " pdb=" C3' U F 23 " ideal model delta sinusoidal sigma weight residual -35.00 2.87 -37.87 1 8.00e+00 1.56e-02 3.16e+01 dihedral pdb=" C4' U F 23 " pdb=" C3' U F 23 " pdb=" C2' U F 23 " pdb=" C1' U F 23 " ideal model delta sinusoidal sigma weight residual -35.00 2.17 -37.17 1 8.00e+00 1.56e-02 3.05e+01 ... (remaining 4559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1240 0.083 - 0.166: 50 0.166 - 0.249: 6 0.249 - 0.332: 1 0.332 - 0.415: 1 Chirality restraints: 1298 Sorted by residual: chirality pdb=" C3' G F 77 " pdb=" C4' G F 77 " pdb=" O3' G F 77 " pdb=" C2' G F 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C3' C F 76 " pdb=" C4' C F 76 " pdb=" O3' C F 76 " pdb=" C2' C F 76 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" P G F 24 " pdb=" OP1 G F 24 " pdb=" OP2 G F 24 " pdb=" O5' G F 24 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1295 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G F 77 " -0.024 2.00e-02 2.50e+03 1.19e-02 4.25e+00 pdb=" N9 G F 77 " 0.024 2.00e-02 2.50e+03 pdb=" C8 G F 77 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G F 77 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G F 77 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G F 77 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G F 77 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G F 77 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G F 77 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G F 77 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G F 77 " -0.010 2.00e-02 2.50e+03 pdb=" C4 G F 77 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 23 " -0.025 2.00e-02 2.50e+03 1.23e-02 3.43e+00 pdb=" N1 U F 23 " 0.021 2.00e-02 2.50e+03 pdb=" C2 U F 23 " 0.008 2.00e-02 2.50e+03 pdb=" O2 U F 23 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U F 23 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U F 23 " -0.009 2.00e-02 2.50e+03 pdb=" O4 U F 23 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U F 23 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U F 23 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 84 " -0.020 2.00e-02 2.50e+03 1.18e-02 3.15e+00 pdb=" N1 U F 84 " 0.029 2.00e-02 2.50e+03 pdb=" C2 U F 84 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U F 84 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U F 84 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U F 84 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U F 84 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U F 84 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U F 84 " 0.000 2.00e-02 2.50e+03 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1382 2.78 - 3.31: 6260 3.31 - 3.84: 13367 3.84 - 4.37: 15153 4.37 - 4.90: 21883 Nonbonded interactions: 58045 Sorted by model distance: nonbonded pdb=" O2' U F 87 " pdb=" O2' U F 90 " model vdw 2.249 3.040 nonbonded pdb=" O ALA A 97 " pdb=" OG1 THR A 101 " model vdw 2.258 3.040 nonbonded pdb=" NE2 GLN A 32 " pdb=" O LYS A 168 " model vdw 2.311 3.120 nonbonded pdb=" OP2 U F 158 " pdb=" OG SER A 26 " model vdw 2.337 3.040 nonbonded pdb=" O2' G F 5 " pdb=" OP1 G F 6 " model vdw 2.346 3.040 ... (remaining 58040 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.930 Find NCS groups from input model: 0.020 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:9.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.003 0.048 7404 Z= 0.146 Angle : 0.583 8.829 10785 Z= 0.325 Chirality : 0.038 0.415 1298 Planarity : 0.004 0.040 779 Dihedral : 24.317 177.673 3740 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.17 (0.42), residues: 427 helix: 1.16 (0.42), residues: 176 sheet: -0.53 (0.61), residues: 75 loop : -1.21 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.014 0.001 TYR A 412 PHE 0.017 0.001 PHE A 143 TRP 0.005 0.001 TRP A 292 HIS 0.006 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7404) covalent geometry : angle 0.58283 (10785) hydrogen bonds : bond 0.12640 ( 305) hydrogen bonds : angle 4.98066 ( 728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.186 Fit side-chains REVERT: A 388 MET cc_start: 0.3144 (ptp) cc_final: 0.2794 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.5042 time to fit residues: 38.8242 Evaluate side-chains 42 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS A 287 GLN A 365 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.253394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.201245 restraints weight = 7472.950| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 1.37 r_work: 0.3832 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7404 Z= 0.141 Angle : 0.596 9.275 10785 Z= 0.311 Chirality : 0.036 0.243 1298 Planarity : 0.004 0.038 779 Dihedral : 25.783 178.114 2862 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.65 % Allowed : 13.50 % Favored : 84.85 % 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: -0.01 (0.42), residues: 427 helix: 1.37 (0.42), residues: 179 sheet: -0.46 (0.62), residues: 76 loop : -1.25 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.033 0.002 TYR A 412 PHE 0.021 0.002 PHE A 143 TRP 0.005 0.001 TRP A 69 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7404) covalent geometry : angle 0.59640 (10785) hydrogen bonds : bond 0.04235 ( 305) hydrogen bonds : angle 3.71076 ( 728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.178 Fit side-chains REVERT: A 58 VAL cc_start: 0.6973 (t) cc_final: 0.6769 (t) REVERT: A 75 MET cc_start: 0.7192 (mtm) cc_final: 0.6561 (mtt) REVERT: A 182 ILE cc_start: 0.6248 (pp) cc_final: 0.5841 (mp) REVERT: A 268 TYR cc_start: 0.6411 (m-80) cc_final: 0.5523 (m-80) REVERT: A 388 MET cc_start: 0.3565 (ptp) cc_final: 0.3259 (mmp) outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.5069 time to fit residues: 22.9792 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 0.0670 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 102 ASN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.254414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.201543 restraints weight = 7422.958| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.38 r_work: 0.3780 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7404 Z= 0.129 Angle : 0.565 9.403 10785 Z= 0.296 Chirality : 0.035 0.236 1298 Planarity : 0.004 0.038 779 Dihedral : 25.581 176.599 2862 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.03 % Allowed : 16.53 % Favored : 80.44 % 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: 0.09 (0.42), residues: 427 helix: 1.45 (0.42), residues: 177 sheet: -0.51 (0.62), residues: 76 loop : -1.11 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.029 0.002 TYR A 412 PHE 0.018 0.002 PHE A 143 TRP 0.008 0.002 TRP A 292 HIS 0.006 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7404) covalent geometry : angle 0.56477 (10785) hydrogen bonds : bond 0.03807 ( 305) hydrogen bonds : angle 3.41321 ( 728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5914 (mp) REVERT: A 268 TYR cc_start: 0.6366 (m-80) cc_final: 0.5220 (m-80) REVERT: A 353 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5976 (tt0) REVERT: A 388 MET cc_start: 0.3597 (ptp) cc_final: 0.3236 (mmp) outliers start: 11 outliers final: 3 residues processed: 49 average time/residue: 0.5016 time to fit residues: 25.8503 Evaluate side-chains 41 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.246034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199375 restraints weight = 7403.433| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.18 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7404 Z= 0.231 Angle : 0.673 9.637 10785 Z= 0.354 Chirality : 0.040 0.334 1298 Planarity : 0.005 0.047 779 Dihedral : 25.691 175.885 2862 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.31 % Allowed : 16.80 % Favored : 79.89 % 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: -0.17 (0.41), residues: 427 helix: 1.15 (0.42), residues: 176 sheet: -0.68 (0.61), residues: 75 loop : -1.10 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.029 0.002 TYR A 412 PHE 0.031 0.003 PHE A 143 TRP 0.010 0.002 TRP A 80 HIS 0.006 0.002 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 7404) covalent geometry : angle 0.67285 (10785) hydrogen bonds : bond 0.04934 ( 305) hydrogen bonds : angle 3.81624 ( 728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6144 (mt) REVERT: A 268 TYR cc_start: 0.6852 (m-80) cc_final: 0.6385 (m-80) REVERT: A 353 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6020 (tt0) outliers start: 12 outliers final: 4 residues processed: 46 average time/residue: 0.5500 time to fit residues: 26.6704 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.243918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193113 restraints weight = 7438.527| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 1.40 r_work: 0.3609 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7404 Z= 0.247 Angle : 0.687 9.188 10785 Z= 0.362 Chirality : 0.041 0.331 1298 Planarity : 0.006 0.069 779 Dihedral : 25.751 175.654 2862 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.58 % Allowed : 19.56 % Favored : 76.86 % 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: -0.48 (0.41), residues: 427 helix: 0.91 (0.41), residues: 176 sheet: -0.85 (0.61), residues: 75 loop : -1.28 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 358 TYR 0.030 0.002 TYR A 412 PHE 0.029 0.003 PHE A 143 TRP 0.010 0.002 TRP A 80 HIS 0.009 0.002 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 7404) covalent geometry : angle 0.68738 (10785) hydrogen bonds : bond 0.05032 ( 305) hydrogen bonds : angle 4.00113 ( 728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6827 (tp30) REVERT: A 65 ASP cc_start: 0.7374 (t0) cc_final: 0.7063 (t0) REVERT: A 75 MET cc_start: 0.8033 (mtm) cc_final: 0.7815 (mtm) REVERT: A 280 THR cc_start: 0.7331 (p) cc_final: 0.7041 (t) REVERT: A 388 MET cc_start: 0.4009 (OUTLIER) cc_final: 0.3044 (ptp) outliers start: 13 outliers final: 5 residues processed: 46 average time/residue: 0.6511 time to fit residues: 31.4543 Evaluate side-chains 43 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 388 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 21 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.247281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.201578 restraints weight = 7425.603| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.06 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7404 Z= 0.167 Angle : 0.607 9.501 10785 Z= 0.320 Chirality : 0.037 0.277 1298 Planarity : 0.004 0.036 779 Dihedral : 25.631 176.561 2862 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.31 % Allowed : 21.21 % Favored : 75.48 % 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: -0.33 (0.41), residues: 427 helix: 1.07 (0.41), residues: 177 sheet: -0.86 (0.61), residues: 75 loop : -1.23 (0.43), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.023 0.002 TYR A 302 PHE 0.020 0.002 PHE A 143 TRP 0.008 0.002 TRP A 80 HIS 0.004 0.002 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7404) covalent geometry : angle 0.60665 (10785) hydrogen bonds : bond 0.04211 ( 305) hydrogen bonds : angle 3.70900 ( 728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5239 (tmt170) REVERT: A 280 THR cc_start: 0.7393 (p) cc_final: 0.7134 (t) REVERT: A 353 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6095 (tt0) REVERT: A 388 MET cc_start: 0.3386 (OUTLIER) cc_final: 0.2961 (ptp) outliers start: 12 outliers final: 3 residues processed: 45 average time/residue: 0.6033 time to fit residues: 28.3853 Evaluate side-chains 40 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 388 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 9 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.247931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.201933 restraints weight = 7376.289| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.05 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7404 Z= 0.152 Angle : 0.595 9.697 10785 Z= 0.314 Chirality : 0.036 0.267 1298 Planarity : 0.004 0.035 779 Dihedral : 25.566 176.774 2862 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.48 % Allowed : 21.49 % Favored : 76.03 % 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: -0.20 (0.41), residues: 427 helix: 1.21 (0.41), residues: 176 sheet: -0.93 (0.62), residues: 76 loop : -1.09 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 291 TYR 0.021 0.002 TYR A 302 PHE 0.020 0.002 PHE A 143 TRP 0.007 0.001 TRP A 80 HIS 0.005 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7404) covalent geometry : angle 0.59495 (10785) hydrogen bonds : bond 0.04050 ( 305) hydrogen bonds : angle 3.60385 ( 728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.6823 (t0) cc_final: 0.6556 (t0) REVERT: A 132 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.5105 (tmt170) REVERT: A 183 TRP cc_start: 0.6610 (m100) cc_final: 0.6103 (m100) REVERT: A 280 THR cc_start: 0.7353 (p) cc_final: 0.7137 (t) REVERT: A 353 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6056 (tt0) outliers start: 9 outliers final: 4 residues processed: 37 average time/residue: 0.6271 time to fit residues: 24.4296 Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 388 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.247596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202563 restraints weight = 7386.918| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.09 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7404 Z= 0.164 Angle : 0.609 9.891 10785 Z= 0.321 Chirality : 0.037 0.278 1298 Planarity : 0.004 0.035 779 Dihedral : 25.526 176.726 2862 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.93 % Allowed : 22.59 % Favored : 75.48 % 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: -0.24 (0.41), residues: 427 helix: 1.15 (0.41), residues: 176 sheet: -0.86 (0.62), residues: 75 loop : -1.14 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.022 0.002 TYR A 302 PHE 0.021 0.002 PHE A 143 TRP 0.007 0.002 TRP A 80 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7404) covalent geometry : angle 0.60851 (10785) hydrogen bonds : bond 0.04125 ( 305) hydrogen bonds : angle 3.62467 ( 728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.6829 (t0) cc_final: 0.6588 (t0) REVERT: A 132 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.5053 (tmt170) REVERT: A 183 TRP cc_start: 0.6697 (m100) cc_final: 0.6273 (m100) REVERT: A 280 THR cc_start: 0.7297 (p) cc_final: 0.7066 (t) REVERT: A 353 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6031 (tt0) REVERT: A 388 MET cc_start: 0.3258 (OUTLIER) cc_final: 0.2924 (ptp) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.6103 time to fit residues: 25.0174 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 388 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.248591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.203466 restraints weight = 7382.105| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.06 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7404 Z= 0.147 Angle : 0.599 9.928 10785 Z= 0.317 Chirality : 0.036 0.261 1298 Planarity : 0.004 0.035 779 Dihedral : 25.478 176.833 2862 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.93 % Allowed : 22.87 % Favored : 75.21 % 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: -0.27 (0.41), residues: 427 helix: 1.07 (0.41), residues: 178 sheet: -0.92 (0.62), residues: 76 loop : -1.09 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.022 0.002 TYR A 302 PHE 0.019 0.002 PHE A 143 TRP 0.010 0.002 TRP A 235 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7404) covalent geometry : angle 0.59950 (10785) hydrogen bonds : bond 0.03970 ( 305) hydrogen bonds : angle 3.58954 ( 728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.6862 (t0) cc_final: 0.6619 (t0) REVERT: A 132 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.4901 (tmt170) REVERT: A 183 TRP cc_start: 0.6716 (m100) cc_final: 0.6296 (m100) REVERT: A 280 THR cc_start: 0.7297 (p) cc_final: 0.7087 (t) REVERT: A 353 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6039 (tt0) REVERT: A 388 MET cc_start: 0.3298 (OUTLIER) cc_final: 0.2978 (ptp) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.5999 time to fit residues: 23.8574 Evaluate side-chains 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 388 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.249168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.205124 restraints weight = 7360.786| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.01 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7404 Z= 0.140 Angle : 0.600 9.984 10785 Z= 0.318 Chirality : 0.036 0.253 1298 Planarity : 0.005 0.038 779 Dihedral : 25.439 176.908 2862 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.93 % Allowed : 23.14 % Favored : 74.93 % 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: -0.23 (0.41), residues: 427 helix: 1.14 (0.41), residues: 176 sheet: -0.94 (0.62), residues: 76 loop : -1.07 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 291 TYR 0.022 0.002 TYR A 302 PHE 0.018 0.002 PHE A 143 TRP 0.018 0.002 TRP A 235 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7404) covalent geometry : angle 0.59961 (10785) hydrogen bonds : bond 0.03932 ( 305) hydrogen bonds : angle 3.53890 ( 728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.4851 (tmt170) REVERT: A 183 TRP cc_start: 0.6738 (m100) cc_final: 0.6458 (m100) REVERT: A 268 TYR cc_start: 0.6920 (m-80) cc_final: 0.6384 (m-80) REVERT: A 280 THR cc_start: 0.7289 (p) cc_final: 0.7070 (t) REVERT: A 353 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6020 (tt0) REVERT: A 388 MET cc_start: 0.3246 (OUTLIER) cc_final: 0.2956 (ptp) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.5501 time to fit residues: 23.3045 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 388 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 30.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.250174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.203525 restraints weight = 7406.011| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.09 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7404 Z= 0.135 Angle : 0.602 10.040 10785 Z= 0.319 Chirality : 0.036 0.243 1298 Planarity : 0.005 0.035 779 Dihedral : 25.392 176.988 2862 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.93 % Allowed : 23.97 % Favored : 74.10 % 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: -0.24 (0.41), residues: 427 helix: 1.02 (0.41), residues: 178 sheet: -0.65 (0.64), residues: 70 loop : -1.12 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 291 TYR 0.023 0.002 TYR A 302 PHE 0.017 0.001 PHE A 143 TRP 0.015 0.002 TRP A 235 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7404) covalent geometry : angle 0.60182 (10785) hydrogen bonds : bond 0.03817 ( 305) hydrogen bonds : angle 3.53969 ( 728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.15 seconds wall clock time: 28 minutes 11.39 seconds (1691.39 seconds total)