Starting phenix.real_space_refine on Tue Aug 4 21:34:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9g_64871/08_2026/9v9g_64871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9g_64871/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9g_64871/08_2026/9v9g_64871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9g_64871/08_2026/9v9g_64871.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9g_64871/08_2026/9v9g_64871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9g_64871/08_2026/9v9g_64871.cif" } 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-2.2rc3-6140/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: 1.59, 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: 0.64 Conformation dependent library (CDL) restraints added in 414.1 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: 0.53 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: 1.55 Time building geometry restraints manager: 0.82 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: 687 0.031 - 0.062: 241 0.062 - 0.093: 72 0.093 - 0.124: 52 0.124 - 0.156: 24 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=" C2' U C 14 " pdb=" C3' U C 14 " pdb=" O2' U C 14 " pdb=" C1' U C 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" C2' U C 7 " pdb=" C3' U C 7 " pdb=" O2' U C 7 " pdb=" C1' U C 7 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.78e-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: 1.430 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.920 ------------------------------------------------------------------------------- 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= 0.230 Angle : 0.626 25.457 9624 Z= 0.393 Chirality : 0.044 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 0.00336 / 0.23 ( 6978) covalent geometry : angle 0.62560 / 0.39 ( 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 : 0.158 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.5218 time to fit residues: 35.5970 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 : 0.192 ------------------------------------------------------------------------------- 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 = 0.164099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121930 restraints weight = 7627.790| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.13 r_work: 0.3116 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0761 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= 0.137 Angle : 0.564 20.126 9624 Z= 0.301 Chirality : 0.042 0.218 1076 Planarity : 0.005 0.047 1141 Dihedral : 15.244 140.217 1271 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.77 % Allowed : 6.96 % Favored : 92.27 % 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: 0.87 (0.31), residues: 758 helix: 1.85 (0.35), residues: 230 sheet: 0.90 (0.40), residues: 179 loop : -0.44 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 758 TYR 0.026 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 0.56448 / 0.30 ( 9624) hydrogen bonds : bond 0.05008 / 3.57 ( 304) hydrogen bonds : angle 5.12444 / 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 : 0.186 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 50 average time/residue: 0.4991 time to fit residues: 26.5634 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 : 0.138 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 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: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.164270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122083 restraints weight = 7550.827| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.15 r_work: 0.3121 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0931 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= 0.131 Angle : 0.525 16.808 9624 Z= 0.284 Chirality : 0.042 0.181 1076 Planarity : 0.004 0.047 1141 Dihedral : 15.232 137.405 1271 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 0.96 (0.31), residues: 758 helix: 1.95 (0.35), residues: 232 sheet: 0.87 (0.39), residues: 179 loop : -0.36 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.017 0.002 TYR A 380 PHE 0.010 0.001 PHE A 545 TRP 0.011 0.001 TRP A 136 HIS 0.008 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6978) covalent geometry : angle 0.52463 / 0.28 ( 9624) hydrogen bonds : bond 0.04619 / 3.29 ( 304) hydrogen bonds : angle 4.86761 / 3.54 ( 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 53 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.9038 (mtp) cc_final: 0.8807 (mtm) REVERT: A 261 ARG cc_start: 0.6693 (ptp-170) cc_final: 0.6290 (ptp-170) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.3889 time to fit residues: 21.3421 Evaluate side-chains 46 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 674 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 = 0.3822 r_free = 0.3822 target = 0.162584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120519 restraints weight = 7665.441| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.14 r_work: 0.3095 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1060 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= 0.147 Angle : 0.535 15.032 9624 Z= 0.290 Chirality : 0.043 0.197 1076 Planarity : 0.004 0.042 1141 Dihedral : 15.270 138.545 1271 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.93 % Allowed : 11.28 % Favored : 87.79 % 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: 0.95 (0.31), residues: 758 helix: 1.97 (0.35), residues: 232 sheet: 0.76 (0.39), residues: 181 loop : -0.34 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.019 0.001 TYR A 380 PHE 0.012 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 0.00323 / 0.15 ( 6978) covalent geometry : angle 0.53536 / 0.29 ( 9624) hydrogen bonds : bond 0.04665 / 3.26 ( 304) hydrogen bonds : angle 4.83123 / 3.52 ( 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 53 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7603 (t0) cc_final: 0.7160 (t0) REVERT: A 218 MET cc_start: 0.9099 (mtp) cc_final: 0.8872 (mtm) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.4237 time to fit residues: 23.1700 Evaluate side-chains 47 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.164953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122697 restraints weight = 7715.196| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.14 r_work: 0.3125 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6978 Z= 0.117 Angle : 0.496 13.770 9624 Z= 0.272 Chirality : 0.041 0.178 1076 Planarity : 0.004 0.035 1141 Dihedral : 15.238 137.869 1271 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.39 % Allowed : 11.59 % Favored : 87.02 % 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: 1.14 (0.31), residues: 758 helix: 2.16 (0.35), residues: 231 sheet: 0.79 (0.39), residues: 192 loop : -0.23 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 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 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 6978) covalent geometry : angle 0.49579 / 0.27 ( 9624) hydrogen bonds : bond 0.04117 / 2.93 ( 304) hydrogen bonds : angle 4.69692 / 3.41 ( 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 52 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.9082 (mtp) cc_final: 0.8865 (mtm) outliers start: 9 outliers final: 3 residues processed: 49 average time/residue: 0.4530 time to fit residues: 23.6299 Evaluate side-chains 45 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.0010 chunk 2 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123414 restraints weight = 7742.848| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.15 r_work: 0.3131 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1255 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= 0.114 Angle : 0.486 12.758 9624 Z= 0.267 Chirality : 0.041 0.178 1076 Planarity : 0.004 0.033 1141 Dihedral : 15.169 137.271 1271 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.39 % Allowed : 11.75 % 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: 1.27 (0.31), residues: 758 helix: 2.28 (0.35), residues: 231 sheet: 0.84 (0.39), residues: 192 loop : -0.14 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.016 0.001 TYR A 380 PHE 0.009 0.001 PHE A 545 TRP 0.009 0.001 TRP A 136 HIS 0.002 0.000 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6978) covalent geometry : angle 0.48626 / 0.27 ( 9624) hydrogen bonds : bond 0.03906 / 2.77 ( 304) hydrogen bonds : angle 4.60863 / 3.34 ( 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 55 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 255 ARG cc_start: 0.7230 (ttt-90) cc_final: 0.6990 (ttt-90) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.4555 time to fit residues: 25.2669 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 551 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN A 674 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 = 0.3809 r_free = 0.3809 target = 0.161240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119198 restraints weight = 7656.244| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.13 r_work: 0.3068 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1251 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= 0.182 Angle : 0.559 13.243 9624 Z= 0.301 Chirality : 0.044 0.202 1076 Planarity : 0.005 0.038 1141 Dihedral : 15.236 137.323 1271 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.24 % Allowed : 12.36 % 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: 1.05 (0.31), residues: 758 helix: 2.08 (0.35), residues: 231 sheet: 0.74 (0.39), 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 0.023 0.002 TYR A 380 PHE 0.014 0.001 PHE A 545 TRP 0.013 0.002 TRP A 620 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 6978) covalent geometry : angle 0.55926 / 0.30 ( 9624) hydrogen bonds : bond 0.04989 / 3.44 ( 304) hydrogen bonds : angle 4.82051 / 3.52 ( 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 54 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7671 (t0) cc_final: 0.7405 (t0) outliers start: 8 outliers final: 2 residues processed: 52 average time/residue: 0.5064 time to fit residues: 28.1262 Evaluate side-chains 44 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 0.0370 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 345 GLN A 590 GLN A 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122748 restraints weight = 7678.205| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.15 r_work: 0.3119 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1312 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= 0.114 Angle : 0.487 12.500 9624 Z= 0.269 Chirality : 0.041 0.179 1076 Planarity : 0.004 0.034 1141 Dihedral : 15.193 137.820 1271 Min Nonbonded Distance : 2.164 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: 1.25 (0.32), residues: 758 helix: 2.29 (0.35), residues: 231 sheet: 0.78 (0.39), residues: 192 loop : -0.14 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.016 0.001 TYR A 380 PHE 0.009 0.001 PHE A 545 TRP 0.011 0.001 TRP A 136 HIS 0.002 0.000 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6978) covalent geometry : angle 0.48681 / 0.27 ( 9624) hydrogen bonds : bond 0.04019 / 2.85 ( 304) hydrogen bonds : angle 4.61259 / 3.36 ( 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 49 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.9117 (mtp) cc_final: 0.8889 (mtm) REVERT: A 255 ARG cc_start: 0.7262 (ttt-90) cc_final: 0.6967 (ttt-90) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.4962 time to fit residues: 24.2782 Evaluate side-chains 46 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.164482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122267 restraints weight = 7673.246| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.16 r_work: 0.3110 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1334 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= 0.124 Angle : 0.496 12.264 9624 Z= 0.272 Chirality : 0.041 0.186 1076 Planarity : 0.004 0.061 1141 Dihedral : 15.142 136.981 1271 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 11.75 % 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: 1.27 (0.32), residues: 758 helix: 2.30 (0.35), residues: 231 sheet: 0.80 (0.39), residues: 192 loop : -0.12 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.018 0.001 TYR A 380 PHE 0.010 0.001 PHE A 545 TRP 0.010 0.001 TRP A 136 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6978) covalent geometry : angle 0.49588 / 0.27 ( 9624) hydrogen bonds : bond 0.04107 / 2.89 ( 304) hydrogen bonds : angle 4.58864 / 3.34 ( 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: 10 poor density : 42 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.9118 (mtp) cc_final: 0.8903 (mtm) REVERT: A 255 ARG cc_start: 0.7201 (ttt-90) cc_final: 0.6901 (ttt-90) REVERT: A 261 ARG cc_start: 0.6823 (ttm170) cc_final: 0.6573 (ttm170) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.5218 time to fit residues: 27.3214 Evaluate side-chains 46 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 676 MET 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: 8.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN 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 = 0.3809 r_free = 0.3809 target = 0.161108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118987 restraints weight = 7634.172| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.14 r_work: 0.3068 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6978 Z= 0.194 Angle : 0.565 13.047 9624 Z= 0.304 Chirality : 0.045 0.203 1076 Planarity : 0.005 0.047 1141 Dihedral : 15.246 136.971 1271 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.08 % Allowed : 11.90 % Favored : 87.02 % 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: 1.07 (0.31), residues: 758 helix: 2.10 (0.35), residues: 231 sheet: 0.76 (0.40), residues: 181 loop : -0.22 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.023 0.002 TYR A 380 PHE 0.015 0.002 PHE A 545 TRP 0.012 0.002 TRP A 136 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 6978) covalent geometry : angle 0.56495 / 0.30 ( 9624) hydrogen bonds : bond 0.05072 / 3.50 ( 304) hydrogen bonds : angle 4.78096 / 3.50 ( 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 51 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7688 (t0) cc_final: 0.7400 (t0) REVERT: A 218 MET cc_start: 0.9145 (mtp) cc_final: 0.8896 (mtm) REVERT: A 255 ARG cc_start: 0.7222 (ttt-90) cc_final: 0.6894 (ttt-90) REVERT: A 261 ARG cc_start: 0.6795 (ttm170) cc_final: 0.6539 (ttm170) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.5463 time to fit residues: 27.8481 Evaluate side-chains 47 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 676 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN 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 = 0.3846 r_free = 0.3846 target = 0.164571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122371 restraints weight = 7627.057| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.15 r_work: 0.3117 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1367 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= 0.116 Angle : 0.493 12.584 9624 Z= 0.271 Chirality : 0.041 0.181 1076 Planarity : 0.004 0.038 1141 Dihedral : 15.186 137.545 1271 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.08 % Allowed : 11.90 % Favored : 87.02 % 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 (0.32), residues: 758 helix: 2.26 (0.35), residues: 231 sheet: 0.81 (0.39), residues: 192 loop : -0.14 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.018 0.001 TYR A 380 PHE 0.010 0.001 PHE A 545 TRP 0.012 0.001 TRP A 136 HIS 0.001 0.000 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 6978) covalent geometry : angle 0.49286 / 0.27 ( 9624) hydrogen bonds : bond 0.04076 / 2.88 ( 304) hydrogen bonds : angle 4.58632 / 3.34 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.55 seconds wall clock time: 32 minutes 31.89 seconds (1951.89 seconds total)