Starting phenix.real_space_refine on Sat May 10 11:22:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcn_37444/05_2025/8wcn_37444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcn_37444/05_2025/8wcn_37444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wcn_37444/05_2025/8wcn_37444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcn_37444/05_2025/8wcn_37444.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcn_37444/05_2025/8wcn_37444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcn_37444/05_2025/8wcn_37444.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.030 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 12 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 3894 2.51 5 N 1061 2.21 5 O 1091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6086 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2982 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 10, 'TRANS': 368} Chain: "B" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2974 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' MG': 1, 'G2P': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {' MG': 1, 'G2P': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.00, per 1000 atoms: 0.82 Number of scatterers: 6086 At special positions: 0 Unit cell: (61.456, 74.148, 124.248, 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 26 16.00 P 12 15.00 Mg 2 11.99 O 1091 8.00 N 1061 7.00 C 3894 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: 1.66 Conformation dependent library (CDL) restraints added in 894.9 milliseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 72.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 46 through 72 removed outlier: 3.523A pdb=" N ARG A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 52 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 99 removed outlier: 3.595A pdb=" N PHE A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 114 through 136 removed outlier: 3.727A pdb=" N ASP A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE A 133 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.501A pdb=" N GLY A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 Processing helix chain 'A' and resid 187 through 232 removed outlier: 3.611A pdb=" N LEU A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.166A pdb=" N TYR A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.522A pdb=" N GLN A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 340 Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.598A pdb=" N LEU A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 31 through 46 Processing helix chain 'B' and resid 46 through 72 Processing helix chain 'B' and resid 77 through 99 removed outlier: 3.513A pdb=" N PHE B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.795A pdb=" N PHE B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 104' Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.558A pdb=" N ARG B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS B 109 " --> pdb=" O SER B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 109' Processing helix chain 'B' and resid 110 through 134 Proline residue: B 116 - end of helix removed outlier: 3.883A pdb=" N ILE B 122 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 133 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.853A pdb=" N PHE B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 232 removed outlier: 3.693A pdb=" N ALA B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 259 Processing helix chain 'B' and resid 271 through 280 removed outlier: 4.047A pdb=" N TYR B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.695A pdb=" N ASP B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.789A pdb=" N GLY B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 4.076A pdb=" N GLY B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 removed outlier: 4.332A pdb=" N ARG B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310 removed outlier: 3.620A pdb=" N LEU A 309 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLU A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 391 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 305 through 308 removed outlier: 3.907A pdb=" N ARG B 391 " --> pdb=" O LEU B 357 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1203 1.33 - 1.46: 2056 1.46 - 1.59: 2893 1.59 - 1.72: 12 1.72 - 1.85: 48 Bond restraints: 6212 Sorted by residual: bond pdb=" CA ASP A 130 " pdb=" C ASP A 130 " ideal model delta sigma weight residual 1.521 1.462 0.058 9.90e-03 1.02e+04 3.46e+01 bond pdb=" N VAL B 390 " pdb=" CA VAL B 390 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.72e+00 bond pdb=" CA ASP B 130 " pdb=" C ASP B 130 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.32e-02 5.74e+03 8.39e+00 bond pdb=" N ARG B 391 " pdb=" CA ARG B 391 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.23e-02 6.61e+03 6.48e+00 bond pdb=" N ASP B 384 " pdb=" CA ASP B 384 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.44e+00 ... (remaining 6207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 8252 1.94 - 3.89: 144 3.89 - 5.83: 38 5.83 - 7.77: 14 7.77 - 9.72: 7 Bond angle restraints: 8455 Sorted by residual: angle pdb=" N GLN B 219 " pdb=" CA GLN B 219 " pdb=" C GLN B 219 " ideal model delta sigma weight residual 112.45 105.11 7.34 1.39e+00 5.18e-01 2.79e+01 angle pdb=" N ALA B 286 " pdb=" CA ALA B 286 " pdb=" C ALA B 286 " ideal model delta sigma weight residual 111.75 106.80 4.95 1.28e+00 6.10e-01 1.49e+01 angle pdb=" CA ARG A 377 " pdb=" CB ARG A 377 " pdb=" CG ARG A 377 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 122.42 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CA ALA B 389 " pdb=" C ALA B 389 " pdb=" O ALA B 389 " ideal model delta sigma weight residual 121.87 118.37 3.50 1.10e+00 8.26e-01 1.01e+01 ... (remaining 8450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 3200 16.86 - 33.71: 347 33.71 - 50.56: 110 50.56 - 67.42: 42 67.42 - 84.27: 8 Dihedral angle restraints: 3707 sinusoidal: 1540 harmonic: 2167 Sorted by residual: dihedral pdb=" CA MET B 366 " pdb=" C MET B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual 180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASP B 130 " pdb=" CB ASP B 130 " pdb=" CG ASP B 130 " pdb=" OD1 ASP B 130 " ideal model delta sinusoidal sigma weight residual -30.00 -89.90 59.90 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CB GLU A 35 " pdb=" CG GLU A 35 " pdb=" CD GLU A 35 " pdb=" OE1 GLU A 35 " ideal model delta sinusoidal sigma weight residual 0.00 -84.27 84.27 1 3.00e+01 1.11e-03 9.60e+00 ... (remaining 3704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 714 0.040 - 0.079: 170 0.079 - 0.119: 50 0.119 - 0.159: 6 0.159 - 0.199: 5 Chirality restraints: 945 Sorted by residual: chirality pdb=" CB ILE B 265 " pdb=" CA ILE B 265 " pdb=" CG1 ILE B 265 " pdb=" CG2 ILE B 265 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CG LEU A 192 " pdb=" CB LEU A 192 " pdb=" CD1 LEU A 192 " pdb=" CD2 LEU A 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA LEU B 148 " pdb=" N LEU B 148 " pdb=" C LEU B 148 " pdb=" CB LEU B 148 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 942 not shown) Planarity restraints: 1064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 218 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C GLU B 218 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU B 218 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN B 219 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 187 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C ASN B 187 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN B 187 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 188 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 242 " 0.121 9.50e-02 1.11e+02 5.53e-02 3.39e+00 pdb=" NE ARG B 242 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 242 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 242 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 242 " -0.003 2.00e-02 2.50e+03 ... (remaining 1061 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 38 2.50 - 3.10: 4380 3.10 - 3.70: 9763 3.70 - 4.30: 12907 4.30 - 4.90: 20597 Nonbonded interactions: 47685 Sorted by model distance: nonbonded pdb=" O1B G2P A 501 " pdb="MG MG A 503 " model vdw 1.902 2.170 nonbonded pdb=" OE2 GLU A 312 " pdb="MG MG A 503 " model vdw 1.982 2.170 nonbonded pdb=" O3B G2P B 501 " pdb="MG MG B 503 " model vdw 2.011 2.170 nonbonded pdb=" OE1 GLU B 312 " pdb="MG MG B 503 " model vdw 2.014 2.170 nonbonded pdb=" O3G G2P A 501 " pdb="MG MG A 503 " model vdw 2.078 2.170 ... (remaining 47680 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 392 or resid 501 through 503)) selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.590 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6212 Z= 0.215 Angle : 0.725 9.717 8455 Z= 0.366 Chirality : 0.040 0.199 945 Planarity : 0.004 0.055 1064 Dihedral : 16.646 84.273 2321 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.50 % Allowed : 19.30 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.30), residues: 753 helix: 0.95 (0.23), residues: 509 sheet: 1.85 (0.57), residues: 59 loop : -1.75 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.002 0.000 HIS B 136 PHE 0.008 0.001 PHE B 103 TYR 0.016 0.001 TYR A 244 ARG 0.022 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.24461 ( 424) hydrogen bonds : angle 7.25728 ( 1263) covalent geometry : bond 0.00357 ( 6212) covalent geometry : angle 0.72473 ( 8455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 303 LEU cc_start: 0.7989 (mt) cc_final: 0.7634 (tt) REVERT: B 41 PHE cc_start: 0.7401 (t80) cc_final: 0.7103 (t80) REVERT: B 313 GLU cc_start: 0.6613 (pp20) cc_final: 0.6280 (pp20) REVERT: B 338 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8021 (mt-10) outliers start: 3 outliers final: 1 residues processed: 121 average time/residue: 0.2454 time to fit residues: 36.2081 Evaluate side-chains 110 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.168483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143414 restraints weight = 10455.716| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.60 r_work: 0.3830 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6212 Z= 0.175 Angle : 0.670 8.432 8455 Z= 0.331 Chirality : 0.045 0.364 945 Planarity : 0.004 0.027 1064 Dihedral : 10.589 82.479 973 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.16 % Allowed : 17.80 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.32), residues: 753 helix: 1.67 (0.23), residues: 514 sheet: 1.66 (0.61), residues: 59 loop : -1.88 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS A 136 PHE 0.016 0.002 PHE B 207 TYR 0.010 0.001 TYR A 244 ARG 0.003 0.001 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.05597 ( 424) hydrogen bonds : angle 4.70586 ( 1263) covalent geometry : bond 0.00386 ( 6212) covalent geometry : angle 0.66969 ( 8455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8203 (p) cc_final: 0.7689 (p) REVERT: A 85 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6100 (tp) REVERT: A 185 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6687 (tm-30) REVERT: A 228 MET cc_start: 0.7960 (ttm) cc_final: 0.7743 (ttm) REVERT: A 377 ARG cc_start: 0.8089 (tpm-80) cc_final: 0.7644 (tpm-80) REVERT: B 63 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6925 (tp) REVERT: B 70 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7970 (ttp) REVERT: B 209 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7176 (tp) REVERT: B 278 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6885 (m-70) outliers start: 25 outliers final: 12 residues processed: 125 average time/residue: 0.2226 time to fit residues: 34.6393 Evaluate side-chains 120 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.167842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.142749 restraints weight = 10439.129| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.69 r_work: 0.3816 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6212 Z= 0.173 Angle : 0.675 10.197 8455 Z= 0.323 Chirality : 0.043 0.326 945 Planarity : 0.003 0.026 1064 Dihedral : 10.016 83.785 973 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 6.16 % Allowed : 18.47 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.31), residues: 753 helix: 1.60 (0.23), residues: 515 sheet: 1.61 (0.62), residues: 59 loop : -2.07 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.007 0.001 HIS B 77 PHE 0.020 0.002 PHE A 81 TYR 0.006 0.001 TYR A 319 ARG 0.005 0.000 ARG B 391 Details of bonding type rmsd hydrogen bonds : bond 0.05333 ( 424) hydrogen bonds : angle 4.57957 ( 1263) covalent geometry : bond 0.00389 ( 6212) covalent geometry : angle 0.67498 ( 8455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7115 (pm20) cc_final: 0.6880 (pm20) REVERT: A 46 SER cc_start: 0.8264 (p) cc_final: 0.7777 (p) REVERT: A 85 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6028 (tp) REVERT: A 185 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6652 (tm-30) REVERT: A 218 GLU cc_start: 0.7361 (tt0) cc_final: 0.6958 (tt0) REVERT: A 228 MET cc_start: 0.8022 (ttm) cc_final: 0.7682 (ttm) REVERT: A 377 ARG cc_start: 0.8124 (tpm-80) cc_final: 0.7717 (tpm-80) REVERT: B 41 PHE cc_start: 0.7770 (t80) cc_final: 0.7413 (t80) REVERT: B 63 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6869 (tp) REVERT: B 70 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8086 (ttp) REVERT: B 209 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7144 (tp) REVERT: B 278 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6885 (m-70) REVERT: B 290 GLN cc_start: 0.7250 (mp10) cc_final: 0.6955 (mp10) REVERT: B 325 ASN cc_start: 0.8331 (t0) cc_final: 0.8125 (t0) REVERT: B 327 LEU cc_start: 0.8996 (mm) cc_final: 0.8792 (mm) REVERT: B 332 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7501 (ptt-90) outliers start: 37 outliers final: 22 residues processed: 131 average time/residue: 0.2119 time to fit residues: 34.8411 Evaluate side-chains 135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.168177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.142948 restraints weight = 10582.857| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.73 r_work: 0.3792 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6212 Z= 0.173 Angle : 0.677 12.466 8455 Z= 0.322 Chirality : 0.044 0.397 945 Planarity : 0.003 0.031 1064 Dihedral : 9.912 85.806 973 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.49 % Allowed : 21.46 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 753 helix: 1.67 (0.23), residues: 514 sheet: 1.35 (0.62), residues: 59 loop : -2.12 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.007 0.001 HIS B 77 PHE 0.015 0.002 PHE A 81 TYR 0.007 0.001 TYR A 244 ARG 0.005 0.000 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 424) hydrogen bonds : angle 4.48866 ( 1263) covalent geometry : bond 0.00391 ( 6212) covalent geometry : angle 0.67724 ( 8455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7263 (pm20) cc_final: 0.7028 (pm20) REVERT: A 46 SER cc_start: 0.8287 (p) cc_final: 0.7848 (p) REVERT: A 85 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.5892 (tp) REVERT: A 185 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6589 (tm-30) REVERT: A 228 MET cc_start: 0.8040 (ttm) cc_final: 0.7672 (ttm) REVERT: A 377 ARG cc_start: 0.8085 (tpm-80) cc_final: 0.7785 (tpm-80) REVERT: B 63 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6908 (tp) REVERT: B 70 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8111 (ttp) REVERT: B 209 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7146 (tp) REVERT: B 278 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6846 (m-70) REVERT: B 290 GLN cc_start: 0.7328 (mp10) cc_final: 0.7038 (mp10) REVERT: B 332 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7483 (ptt-90) outliers start: 33 outliers final: 21 residues processed: 128 average time/residue: 0.2309 time to fit residues: 36.6483 Evaluate side-chains 135 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 332 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 69 optimal weight: 0.0070 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.169649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145651 restraints weight = 10363.599| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.67 r_work: 0.3822 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6212 Z= 0.140 Angle : 0.694 14.332 8455 Z= 0.319 Chirality : 0.042 0.382 945 Planarity : 0.003 0.031 1064 Dihedral : 9.686 87.993 973 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.49 % Allowed : 23.63 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.32), residues: 753 helix: 1.80 (0.23), residues: 515 sheet: 1.32 (0.63), residues: 59 loop : -2.07 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 61 HIS 0.006 0.001 HIS B 77 PHE 0.015 0.001 PHE A 81 TYR 0.008 0.001 TYR A 319 ARG 0.004 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 424) hydrogen bonds : angle 4.35822 ( 1263) covalent geometry : bond 0.00302 ( 6212) covalent geometry : angle 0.69369 ( 8455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7277 (pm20) cc_final: 0.7043 (pm20) REVERT: A 46 SER cc_start: 0.8253 (p) cc_final: 0.7828 (p) REVERT: A 85 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.5924 (tp) REVERT: A 185 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: A 228 MET cc_start: 0.8050 (ttm) cc_final: 0.7703 (ttm) REVERT: A 235 LEU cc_start: 0.8748 (tt) cc_final: 0.8523 (tt) REVERT: A 366 MET cc_start: 0.7146 (ppp) cc_final: 0.6788 (tmm) REVERT: A 377 ARG cc_start: 0.8075 (tpm-80) cc_final: 0.7753 (tpm-80) REVERT: B 63 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6889 (tp) REVERT: B 209 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7166 (tp) REVERT: B 278 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6779 (m-70) REVERT: B 290 GLN cc_start: 0.7282 (mp10) cc_final: 0.6973 (mp10) REVERT: B 338 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7220 (mt-10) REVERT: B 366 MET cc_start: 0.7592 (tmm) cc_final: 0.7366 (tmm) REVERT: B 383 LYS cc_start: 0.8360 (tptp) cc_final: 0.7575 (mmmt) outliers start: 33 outliers final: 19 residues processed: 127 average time/residue: 0.2225 time to fit residues: 35.4549 Evaluate side-chains 130 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 23 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.168578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143563 restraints weight = 10337.012| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.71 r_work: 0.3815 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6212 Z= 0.145 Angle : 0.681 15.423 8455 Z= 0.318 Chirality : 0.043 0.368 945 Planarity : 0.003 0.046 1064 Dihedral : 9.609 89.502 973 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.99 % Allowed : 22.96 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.31), residues: 753 helix: 1.87 (0.23), residues: 510 sheet: 1.33 (0.64), residues: 59 loop : -2.06 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.006 0.001 HIS B 77 PHE 0.019 0.002 PHE A 81 TYR 0.008 0.001 TYR A 244 ARG 0.005 0.000 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 424) hydrogen bonds : angle 4.36542 ( 1263) covalent geometry : bond 0.00317 ( 6212) covalent geometry : angle 0.68113 ( 8455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8257 (p) cc_final: 0.7838 (p) REVERT: A 85 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6121 (tp) REVERT: A 185 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: A 228 MET cc_start: 0.8038 (ttm) cc_final: 0.7703 (ttm) REVERT: A 235 LEU cc_start: 0.8825 (tt) cc_final: 0.8584 (tt) REVERT: A 288 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7857 (mm) REVERT: A 377 ARG cc_start: 0.8060 (tpm-80) cc_final: 0.7740 (tpm-80) REVERT: B 28 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6715 (mp) REVERT: B 63 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6890 (tp) REVERT: B 209 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7186 (tp) REVERT: B 278 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6829 (m-70) REVERT: B 290 GLN cc_start: 0.7319 (mp10) cc_final: 0.6990 (mp10) REVERT: B 308 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6750 (ptm160) REVERT: B 332 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7379 (ptt-90) REVERT: B 383 LYS cc_start: 0.8357 (tptp) cc_final: 0.7614 (mmmt) outliers start: 36 outliers final: 23 residues processed: 125 average time/residue: 0.2316 time to fit residues: 35.9889 Evaluate side-chains 134 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 332 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.0270 chunk 64 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.168768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144382 restraints weight = 10281.695| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.69 r_work: 0.3826 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6212 Z= 0.134 Angle : 0.680 14.307 8455 Z= 0.315 Chirality : 0.042 0.395 945 Planarity : 0.004 0.060 1064 Dihedral : 9.469 88.399 973 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.83 % Allowed : 24.29 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.32), residues: 753 helix: 2.00 (0.23), residues: 516 sheet: 1.32 (0.64), residues: 59 loop : -2.17 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.006 0.001 HIS B 77 PHE 0.017 0.001 PHE A 81 TYR 0.008 0.001 TYR A 319 ARG 0.006 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 424) hydrogen bonds : angle 4.28683 ( 1263) covalent geometry : bond 0.00289 ( 6212) covalent geometry : angle 0.67988 ( 8455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8242 (p) cc_final: 0.7835 (p) REVERT: A 85 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.5969 (tp) REVERT: A 185 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: A 377 ARG cc_start: 0.8050 (tpm-80) cc_final: 0.7762 (tpm-80) REVERT: B 28 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6652 (mp) REVERT: B 63 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6888 (tp) REVERT: B 209 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7167 (tp) REVERT: B 223 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7358 (ttm110) REVERT: B 278 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6845 (m-70) REVERT: B 290 GLN cc_start: 0.7330 (mp10) cc_final: 0.6991 (mp10) REVERT: B 332 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7320 (ptt-90) REVERT: B 338 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 383 LYS cc_start: 0.8330 (tptp) cc_final: 0.7566 (mmmt) outliers start: 29 outliers final: 19 residues processed: 122 average time/residue: 0.2494 time to fit residues: 37.9030 Evaluate side-chains 127 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 332 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.168289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.144043 restraints weight = 10356.363| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.71 r_work: 0.3823 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6212 Z= 0.138 Angle : 0.682 12.713 8455 Z= 0.320 Chirality : 0.043 0.398 945 Planarity : 0.003 0.027 1064 Dihedral : 9.373 87.247 973 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.32 % Allowed : 24.79 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.32), residues: 753 helix: 2.00 (0.23), residues: 516 sheet: 1.29 (0.65), residues: 59 loop : -2.15 (0.46), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 61 HIS 0.005 0.001 HIS B 77 PHE 0.016 0.001 PHE A 81 TYR 0.009 0.001 TYR A 244 ARG 0.009 0.000 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 424) hydrogen bonds : angle 4.27740 ( 1263) covalent geometry : bond 0.00299 ( 6212) covalent geometry : angle 0.68238 ( 8455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8251 (p) cc_final: 0.7844 (p) REVERT: A 85 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6115 (tp) REVERT: A 185 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: A 288 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 377 ARG cc_start: 0.8048 (tpm-80) cc_final: 0.7718 (tpm-80) REVERT: B 28 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6665 (mp) REVERT: B 41 PHE cc_start: 0.7606 (t80) cc_final: 0.7319 (t80) REVERT: B 63 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6885 (tp) REVERT: B 85 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6132 (tt) REVERT: B 209 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7172 (tp) REVERT: B 278 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6847 (m-70) REVERT: B 290 GLN cc_start: 0.7329 (mp10) cc_final: 0.6985 (mp10) REVERT: B 308 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6768 (ptm160) REVERT: B 332 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7299 (ptt-90) outliers start: 32 outliers final: 21 residues processed: 127 average time/residue: 0.2429 time to fit residues: 38.5692 Evaluate side-chains 136 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 332 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.167275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142414 restraints weight = 10372.907| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.73 r_work: 0.3801 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6212 Z= 0.159 Angle : 0.702 11.919 8455 Z= 0.329 Chirality : 0.044 0.399 945 Planarity : 0.004 0.093 1064 Dihedral : 9.424 86.148 973 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.32 % Allowed : 24.79 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.31), residues: 753 helix: 1.93 (0.23), residues: 516 sheet: 1.21 (0.64), residues: 59 loop : -2.22 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.006 0.001 HIS B 77 PHE 0.015 0.002 PHE A 81 TYR 0.008 0.001 TYR A 244 ARG 0.006 0.000 ARG B 391 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 424) hydrogen bonds : angle 4.34062 ( 1263) covalent geometry : bond 0.00359 ( 6212) covalent geometry : angle 0.70207 ( 8455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8263 (p) cc_final: 0.7848 (p) REVERT: A 85 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6130 (tp) REVERT: A 91 MET cc_start: 0.5467 (mmp) cc_final: 0.5267 (mmp) REVERT: A 185 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: A 288 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7845 (mm) REVERT: A 377 ARG cc_start: 0.8063 (tpm-80) cc_final: 0.7735 (tpm-80) REVERT: B 28 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6737 (mp) REVERT: B 63 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6882 (tp) REVERT: B 85 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6169 (tp) REVERT: B 209 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7140 (tp) REVERT: B 223 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7106 (ptp-170) REVERT: B 278 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6902 (m-70) REVERT: B 290 GLN cc_start: 0.7413 (mp10) cc_final: 0.7062 (mp10) REVERT: B 308 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6772 (ptm160) REVERT: B 332 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7320 (ptt-90) outliers start: 32 outliers final: 21 residues processed: 124 average time/residue: 0.2592 time to fit residues: 39.9405 Evaluate side-chains 132 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 332 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.167965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.143246 restraints weight = 10268.550| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.71 r_work: 0.3807 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6212 Z= 0.154 Angle : 0.710 11.465 8455 Z= 0.335 Chirality : 0.044 0.395 945 Planarity : 0.005 0.127 1064 Dihedral : 9.370 85.465 973 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.32 % Allowed : 25.12 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 753 helix: 1.92 (0.23), residues: 516 sheet: 0.73 (0.63), residues: 63 loop : -2.26 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.006 0.001 HIS B 77 PHE 0.015 0.002 PHE A 81 TYR 0.009 0.001 TYR A 244 ARG 0.012 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 424) hydrogen bonds : angle 4.32757 ( 1263) covalent geometry : bond 0.00345 ( 6212) covalent geometry : angle 0.70995 ( 8455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7101 (pm20) cc_final: 0.6831 (pm20) REVERT: A 46 SER cc_start: 0.8242 (p) cc_final: 0.7846 (p) REVERT: A 85 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.5945 (tp) REVERT: A 185 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: A 228 MET cc_start: 0.7990 (ttm) cc_final: 0.7646 (ttm) REVERT: A 288 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 377 ARG cc_start: 0.8099 (tpm-80) cc_final: 0.7757 (tpm-80) REVERT: B 28 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6700 (mp) REVERT: B 85 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6149 (tp) REVERT: B 209 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7135 (tp) REVERT: B 223 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7072 (ptp-170) REVERT: B 278 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6915 (m-70) REVERT: B 290 GLN cc_start: 0.7423 (mp10) cc_final: 0.7068 (mp10) REVERT: B 308 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6874 (ptm160) REVERT: B 332 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7344 (ptt-90) REVERT: B 366 MET cc_start: 0.7660 (tmm) cc_final: 0.7379 (tmm) outliers start: 32 outliers final: 21 residues processed: 127 average time/residue: 0.2634 time to fit residues: 41.1145 Evaluate side-chains 131 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 332 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.168504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144454 restraints weight = 10453.910| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.73 r_work: 0.3811 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6212 Z= 0.158 Angle : 0.732 11.319 8455 Z= 0.340 Chirality : 0.044 0.397 945 Planarity : 0.004 0.083 1064 Dihedral : 9.390 86.696 973 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.16 % Allowed : 25.46 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.31), residues: 753 helix: 1.89 (0.23), residues: 516 sheet: 0.69 (0.64), residues: 63 loop : -2.36 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.006 0.001 HIS B 77 PHE 0.015 0.002 PHE A 81 TYR 0.010 0.001 TYR A 244 ARG 0.007 0.001 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 424) hydrogen bonds : angle 4.35679 ( 1263) covalent geometry : bond 0.00355 ( 6212) covalent geometry : angle 0.73193 ( 8455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.23 seconds wall clock time: 50 minutes 58.24 seconds (3058.24 seconds total)