Starting phenix.real_space_refine on Thu Jul 2 05:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9g_64871/07_2026/9v9g_64871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9g_64871/07_2026/9v9g_64871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v9g_64871/07_2026/9v9g_64871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9g_64871/07_2026/9v9g_64871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v9g_64871/07_2026/9v9g_64871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9g_64871/07_2026/9v9g_64871.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 3 5.21 5 S 15 5.16 5 C 4148 2.51 5 N 1228 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6052 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 42, 'TRANS': 717} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 16} Link IDs: {None: 18} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.23 Number of scatterers: 6784 At special positions: 0 Unit cell: (74.888, 88.504, 102.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 34 15.00 Mg 3 11.99 O 1356 8.00 N 1228 7.00 C 4148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 360.6 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 33.0% alpha, 23.0% beta 8 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.027A pdb=" N ALA A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.619A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 621 through 638 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 749 through 762 removed outlier: 4.366A pdb=" N SER A 755 " --> pdb=" O THR A 751 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 5.536A pdb=" N ARG A 137 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE A 144 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.729A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU A 99 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ARG A 27 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 97 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 239 removed outlier: 3.756A pdb=" N GLY A 234 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA A 272 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 442 removed outlier: 7.282A pdb=" N TYR A 442 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR A 406 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 575 removed outlier: 6.137A pdb=" N LEU A 551 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1841 1.33 - 1.45: 1331 1.45 - 1.57: 3717 1.57 - 1.69: 66 1.69 - 1.81: 23 Bond restraints: 6978 Sorted by residual: bond pdb=" C3' DA B 10 " pdb=" C2' DA B 10 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.53e+00 bond pdb=" C3' DG B 11 " pdb=" C2' DG B 11 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.41e+00 bond pdb=" C3' DT B 14 " pdb=" C2' DT B 14 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.40e+00 bond pdb=" C3' DT B 18 " pdb=" C2' DT B 18 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.91e+00 bond pdb=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.97e+00 ... (remaining 6973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.09: 9618 5.09 - 10.18: 5 10.18 - 15.27: 0 15.27 - 20.37: 0 20.37 - 25.46: 1 Bond angle restraints: 9624 Sorted by residual: angle pdb=" O4' DG B 4 " pdb=" C4' DG B 4 " pdb=" C3' DG B 4 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" C LEU A 577 " pdb=" CA LEU A 577 " pdb=" CB LEU A 577 " ideal model delta sigma weight residual 115.89 110.29 5.60 1.32e+00 5.74e-01 1.80e+01 angle pdb=" C GLN A 260 " pdb=" N ARG A 261 " pdb=" CA ARG A 261 " ideal model delta sigma weight residual 122.56 115.28 7.28 1.72e+00 3.38e-01 1.79e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 9619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 3929 26.91 - 53.81: 196 53.81 - 80.72: 33 80.72 - 107.62: 0 107.62 - 134.53: 1 Dihedral angle restraints: 4159 sinusoidal: 1967 harmonic: 2192 Sorted by residual: dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 85.47 134.53 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" CA TYR A 543 " pdb=" C TYR A 543 " pdb=" N ASP A 544 " pdb=" CA ASP A 544 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLY A 224 " pdb=" C GLY A 224 " pdb=" N LYS A 225 " pdb=" CA LYS A 225 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 4156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 704 0.031 - 0.062: 241 0.062 - 0.093: 70 0.093 - 0.124: 52 0.124 - 0.156: 9 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA ASP A 329 " pdb=" N ASP A 329 " pdb=" C ASP A 329 " pdb=" CB ASP A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE A 689 " pdb=" N ILE A 689 " pdb=" C ILE A 689 " pdb=" CB ILE A 689 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ARG A 261 " pdb=" N ARG A 261 " pdb=" C ARG A 261 " pdb=" CB ARG A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1073 not shown) Planarity restraints: 1141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 470 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO A 471 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 471 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 471 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 257 " -0.020 2.00e-02 2.50e+03 1.32e-02 3.50e+00 pdb=" CG TYR A 257 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 257 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 257 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 257 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 257 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 257 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 257 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 533 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 534 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.023 5.00e-02 4.00e+02 ... (remaining 1138 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 559 2.74 - 3.28: 5977 3.28 - 3.82: 10839 3.82 - 4.36: 13865 4.36 - 4.90: 23046 Nonbonded interactions: 54286 Sorted by model distance: nonbonded pdb=" OG SER A 125 " pdb=" O TRP A 140 " model vdw 2.204 3.040 nonbonded pdb=" OP1 U C 7 " pdb="MG MG A 803 " model vdw 2.260 2.170 nonbonded pdb=" O PRO A 309 " pdb=" O HOH A 901 " model vdw 2.285 3.040 nonbonded pdb=" NE2 GLN A 576 " pdb=" O LYS A 585 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASP A 544 " pdb=" O HOH A 902 " model vdw 2.298 3.040 ... (remaining 54281 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: 1.070 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 6978 Z= 0.228 Angle : 0.602 25.457 9624 Z= 0.370 Chirality : 0.041 0.156 1076 Planarity : 0.005 0.052 1141 Dihedral : 15.492 134.526 2747 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.69 (0.31), residues: 758 helix: 1.57 (0.35), residues: 221 sheet: 0.75 (0.40), residues: 185 loop : -0.37 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.031 0.002 TYR A 257 PHE 0.012 0.001 PHE A 545 TRP 0.014 0.001 TRP A 620 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.23 ( 6978) covalent geometry : angle 0.60176 / 0.37 ( 9624) hydrogen bonds : bond 0.15133 / 11.34 ( 304) hydrogen bonds : angle 6.42736 / 4.64 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.247 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.6032 time to fit residues: 41.1617 Evaluate side-chains 42 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 684 ASN A 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121968 restraints weight = 7625.177| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.13 r_work: 0.3115 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6978 Z= 0.136 Angle : 0.563 20.104 9624 Z= 0.301 Chirality : 0.042 0.231 1076 Planarity : 0.005 0.046 1141 Dihedral : 15.327 140.500 1271 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.77 % Allowed : 6.80 % Favored : 92.43 % 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 (0.31), residues: 758 helix: 1.84 (0.35), residues: 230 sheet: 0.89 (0.40), residues: 179 loop : -0.44 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 758 TYR 0.027 0.002 TYR A 257 PHE 0.011 0.001 PHE A 545 TRP 0.011 0.001 TRP A 136 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 6978) covalent geometry : angle 0.56283 / 0.30 ( 9624) hydrogen bonds : bond 0.04997 / 3.56 ( 304) hydrogen bonds : angle 5.13151 / 3.74 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.238 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 50 average time/residue: 0.5616 time to fit residues: 29.7724 Evaluate side-chains 44 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS A 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120128 restraints weight = 7546.932| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.13 r_work: 0.3091 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6978 Z= 0.157 Angle : 0.551 16.948 9624 Z= 0.298 Chirality : 0.043 0.194 1076 Planarity : 0.005 0.047 1141 Dihedral : 15.388 137.749 1271 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.08 % Allowed : 9.27 % Favored : 89.64 % 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: 0.86 (0.31), residues: 758 helix: 1.85 (0.35), residues: 232 sheet: 0.81 (0.39), residues: 179 loop : -0.41 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 261 TYR 0.019 0.002 TYR A 380 PHE 0.012 0.001 PHE A 545 TRP 0.013 0.001 TRP A 136 HIS 0.008 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 6978) covalent geometry : angle 0.55143 / 0.30 ( 9624) hydrogen bonds : bond 0.05033 / 3.54 ( 304) hydrogen bonds : angle 4.94788 / 3.61 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.9071 (mtp) cc_final: 0.8826 (mtm) REVERT: A 261 ARG cc_start: 0.6756 (ptp-170) cc_final: 0.6334 (ptp-170) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.4917 time to fit residues: 25.6213 Evaluate side-chains 44 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 ASN A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122923 restraints weight = 7669.986| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.17 r_work: 0.3129 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6978 Z= 0.115 Angle : 0.498 14.999 9624 Z= 0.273 Chirality : 0.041 0.182 1076 Planarity : 0.004 0.037 1141 Dihedral : 15.352 138.865 1271 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.93 % Allowed : 11.13 % Favored : 87.94 % 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: 1.06 (0.31), residues: 758 helix: 2.05 (0.35), residues: 232 sheet: 0.84 (0.38), residues: 190 loop : -0.31 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.016 0.001 TYR A 380 PHE 0.009 0.001 PHE A 545 TRP 0.010 0.001 TRP A 136 HIS 0.002 0.000 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 6978) covalent geometry : angle 0.49829 / 0.27 ( 9624) hydrogen bonds : bond 0.04094 / 2.92 ( 304) hydrogen bonds : angle 4.71533 / 3.43 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.9048 (mtp) cc_final: 0.8822 (mtm) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.4381 time to fit residues: 22.9851 Evaluate side-chains 47 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119575 restraints weight = 7733.953| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.16 r_work: 0.3077 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6978 Z= 0.173 Angle : 0.547 14.272 9624 Z= 0.297 Chirality : 0.044 0.200 1076 Planarity : 0.005 0.037 1141 Dihedral : 15.349 138.255 1271 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.24 % Allowed : 12.21 % Favored : 86.55 % 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: 0.96 (0.31), residues: 758 helix: 1.99 (0.35), residues: 231 sheet: 0.76 (0.40), residues: 181 loop : -0.33 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.021 0.002 TYR A 380 PHE 0.014 0.001 PHE A 545 TRP 0.012 0.001 TRP A 136 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 6978) covalent geometry : angle 0.54716 / 0.30 ( 9624) hydrogen bonds : bond 0.04834 / 3.35 ( 304) hydrogen bonds : angle 4.83384 / 3.53 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7641 (t0) cc_final: 0.7193 (t0) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.4281 time to fit residues: 23.4248 Evaluate side-chains 47 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121619 restraints weight = 7756.699| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.15 r_work: 0.3104 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6978 Z= 0.120 Angle : 0.496 13.415 9624 Z= 0.273 Chirality : 0.041 0.183 1076 Planarity : 0.004 0.035 1141 Dihedral : 15.319 138.506 1271 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.24 % Allowed : 11.90 % Favored : 86.86 % 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: 1.12 (0.31), residues: 758 helix: 2.16 (0.35), residues: 231 sheet: 0.76 (0.39), residues: 192 loop : -0.22 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 573 TYR 0.017 0.001 TYR A 380 PHE 0.010 0.001 PHE A 545 TRP 0.011 0.001 TRP A 136 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 6978) covalent geometry : angle 0.49573 / 0.27 ( 9624) hydrogen bonds : bond 0.04178 / 2.95 ( 304) hydrogen bonds : angle 4.69836 / 3.42 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.276 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.5329 time to fit residues: 27.8063 Evaluate side-chains 48 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 676 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 23 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 GLN A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121121 restraints weight = 7664.575| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.17 r_work: 0.3100 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6978 Z= 0.143 Angle : 0.514 13.139 9624 Z= 0.281 Chirality : 0.042 0.192 1076 Planarity : 0.004 0.037 1141 Dihedral : 15.295 138.032 1271 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.85 % Allowed : 11.59 % Favored : 86.55 % 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: 1.11 (0.31), residues: 758 helix: 2.15 (0.35), residues: 231 sheet: 0.79 (0.40), residues: 181 loop : -0.23 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 573 TYR 0.019 0.001 TYR A 380 PHE 0.012 0.001 PHE A 545 TRP 0.011 0.001 TRP A 136 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6978) covalent geometry : angle 0.51422 / 0.28 ( 9624) hydrogen bonds : bond 0.04425 / 3.09 ( 304) hydrogen bonds : angle 4.72698 / 3.44 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7554 (t0) cc_final: 0.7094 (t0) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.4499 time to fit residues: 26.5587 Evaluate side-chains 51 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 676 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.0970 chunk 8 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 590 GLN A 674 ASN A 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124405 restraints weight = 7676.853| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.09 r_work: 0.3147 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6978 Z= 0.105 Angle : 0.472 12.350 9624 Z= 0.262 Chirality : 0.040 0.174 1076 Planarity : 0.004 0.034 1141 Dihedral : 15.243 137.634 1271 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.93 % Allowed : 12.67 % Favored : 86.40 % 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: 1.34 (0.31), residues: 758 helix: 2.37 (0.35), residues: 231 sheet: 0.91 (0.39), residues: 190 loop : -0.14 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.014 0.001 TYR A 380 PHE 0.008 0.001 PHE A 545 TRP 0.011 0.001 TRP A 570 HIS 0.001 0.000 HIS A 736 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 6978) covalent geometry : angle 0.47177 / 0.26 ( 9624) hydrogen bonds : bond 0.03687 / 2.63 ( 304) hydrogen bonds : angle 4.54180 / 3.29 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.250 Fit side-chains REVERT: A 218 MET cc_start: 0.9081 (mtp) cc_final: 0.8864 (mtm) REVERT: A 255 ARG cc_start: 0.7216 (ttt-90) cc_final: 0.6935 (ttt-90) REVERT: A 318 GLU cc_start: 0.7968 (tp30) cc_final: 0.7653 (mp0) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.5258 time to fit residues: 26.8023 Evaluate side-chains 49 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 492 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 GLN A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120840 restraints weight = 7690.074| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.16 r_work: 0.3087 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6978 Z= 0.150 Angle : 0.515 12.581 9624 Z= 0.281 Chirality : 0.042 0.190 1076 Planarity : 0.004 0.035 1141 Dihedral : 15.229 137.572 1271 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.08 % Allowed : 12.21 % Favored : 86.71 % 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 (0.31), residues: 758 helix: 2.24 (0.35), residues: 231 sheet: 0.82 (0.39), residues: 181 loop : -0.20 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.021 0.002 TYR A 380 PHE 0.012 0.001 PHE A 545 TRP 0.010 0.001 TRP A 620 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6978) covalent geometry : angle 0.51470 / 0.28 ( 9624) hydrogen bonds : bond 0.04404 / 3.07 ( 304) hydrogen bonds : angle 4.65250 / 3.39 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7555 (t0) cc_final: 0.7073 (t0) REVERT: A 218 MET cc_start: 0.9120 (mtp) cc_final: 0.8894 (mtm) REVERT: A 255 ARG cc_start: 0.7247 (ttt-90) cc_final: 0.6948 (ttt-90) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.5469 time to fit residues: 29.5384 Evaluate side-chains 48 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 492 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 590 GLN A 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.164099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121952 restraints weight = 7628.207| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.15 r_work: 0.3104 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6978 Z= 0.122 Angle : 0.496 12.795 9624 Z= 0.272 Chirality : 0.041 0.180 1076 Planarity : 0.004 0.036 1141 Dihedral : 15.231 138.208 1271 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.93 % Allowed : 12.67 % Favored : 86.40 % 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: 1.26 (0.31), residues: 758 helix: 2.31 (0.35), residues: 231 sheet: 0.79 (0.38), residues: 192 loop : -0.13 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.019 0.001 TYR A 380 PHE 0.010 0.001 PHE A 545 TRP 0.018 0.001 TRP A 65 HIS 0.002 0.000 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6978) covalent geometry : angle 0.49621 / 0.27 ( 9624) hydrogen bonds : bond 0.04130 / 2.90 ( 304) hydrogen bonds : angle 4.61050 / 3.36 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.9117 (mtp) cc_final: 0.8893 (mtm) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.5082 time to fit residues: 25.9126 Evaluate side-chains 48 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 492 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 GLN A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122076 restraints weight = 7616.492| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.16 r_work: 0.3102 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6978 Z= 0.126 Angle : 0.497 13.912 9624 Z= 0.271 Chirality : 0.041 0.186 1076 Planarity : 0.004 0.035 1141 Dihedral : 15.203 137.484 1271 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.08 % Allowed : 12.36 % Favored : 86.55 % 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: 1.24 (0.31), residues: 758 helix: 2.31 (0.35), residues: 231 sheet: 0.82 (0.39), residues: 181 loop : -0.17 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.019 0.001 TYR A 380 PHE 0.010 0.001 PHE A 545 TRP 0.010 0.001 TRP A 136 HIS 0.002 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 6978) covalent geometry : angle 0.49720 / 0.27 ( 9624) hydrogen bonds : bond 0.04104 / 2.88 ( 304) hydrogen bonds : angle 4.58701 / 3.34 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.02 seconds wall clock time: 34 minutes 43.85 seconds (2083.85 seconds total)