Starting phenix.real_space_refine on Fri Aug 22 16:48:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcn_37444/08_2025/8wcn_37444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcn_37444/08_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_37444/08_2025/8wcn_37444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcn_37444/08_2025/8wcn_37444.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcn_37444/08_2025/8wcn_37444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcn_37444/08_2025/8wcn_37444.cif" } resolution = 3.2 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.68, per 1000 atoms: 0.28 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: 0.49 Conformation dependent library (CDL) restraints added in 288.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.16 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: 0.84 Time building geometry restraints manager: 0.60 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 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: 0.000 Normalize map: mean=0, sd=1: 3.710 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.022 0.001 ARG B 242 TYR 0.016 0.001 TYR A 244 PHE 0.008 0.001 PHE B 103 TRP 0.008 0.001 TRP B 99 HIS 0.002 0.000 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6212) covalent geometry : angle 0.72473 ( 8455) hydrogen bonds : bond 0.24461 ( 424) hydrogen bonds : angle 7.25728 ( 1263) *********************** 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 : 0.223 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: 0.1088 time to fit residues: 16.2464 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 : 0.260 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.0050 chunk 27 optimal weight: 0.9980 overall best weight: 0.2532 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.172433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.147174 restraints weight = 10646.727| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.70 r_work: 0.3891 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6212 Z= 0.141 Angle : 0.647 8.843 8455 Z= 0.316 Chirality : 0.043 0.341 945 Planarity : 0.004 0.029 1064 Dihedral : 10.338 83.504 973 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.16 % Allowed : 19.13 % Favored : 77.70 % 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 aren not related in a simple way. whole: 1.48 (0.32), residues: 753 helix: 1.88 (0.24), residues: 511 sheet: 1.75 (0.62), residues: 54 loop : -1.88 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 334 TYR 0.011 0.001 TYR A 244 PHE 0.012 0.001 PHE B 207 TRP 0.009 0.001 TRP A 61 HIS 0.002 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6212) covalent geometry : angle 0.64676 ( 8455) hydrogen bonds : bond 0.05256 ( 424) hydrogen bonds : angle 4.61369 ( 1263) *********************** 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 129 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.7936 (ttm) cc_final: 0.7730 (ttm) REVERT: A 377 ARG cc_start: 0.8098 (tpm-80) cc_final: 0.7616 (tpm-80) REVERT: B 63 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6906 (tp) REVERT: B 70 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7930 (ttp) REVERT: B 180 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7601 (mm) REVERT: B 238 LEU cc_start: 0.8027 (mp) cc_final: 0.7783 (mt) REVERT: B 325 ASN cc_start: 0.8290 (t0) cc_final: 0.8056 (t0) REVERT: B 366 MET cc_start: 0.7699 (tmm) cc_final: 0.7447 (tmm) outliers start: 19 outliers final: 8 residues processed: 121 average time/residue: 0.0967 time to fit residues: 14.7659 Evaluate side-chains 114 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU 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 130 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 265 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.171989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.147395 restraints weight = 10369.117| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.71 r_work: 0.3864 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6212 Z= 0.136 Angle : 0.634 9.964 8455 Z= 0.302 Chirality : 0.042 0.305 945 Planarity : 0.003 0.025 1064 Dihedral : 9.745 84.578 973 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.16 % Allowed : 18.14 % Favored : 76.71 % 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 aren not related in a simple way. whole: 1.51 (0.32), residues: 753 helix: 1.93 (0.23), residues: 514 sheet: 1.56 (0.64), residues: 54 loop : -1.97 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 391 TYR 0.007 0.001 TYR A 319 PHE 0.018 0.001 PHE B 272 TRP 0.006 0.001 TRP B 61 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6212) covalent geometry : angle 0.63390 ( 8455) hydrogen bonds : bond 0.04807 ( 424) hydrogen bonds : angle 4.43414 ( 1263) *********************** 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 137 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7167 (pm20) cc_final: 0.6903 (pm20) REVERT: A 46 SER cc_start: 0.8239 (p) cc_final: 0.7763 (p) REVERT: A 85 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.5794 (tt) REVERT: A 218 GLU cc_start: 0.7280 (tt0) cc_final: 0.6598 (tt0) REVERT: A 228 MET cc_start: 0.8047 (ttm) cc_final: 0.7673 (ttm) REVERT: A 377 ARG cc_start: 0.8126 (tpm-80) cc_final: 0.7711 (tpm-80) REVERT: B 41 PHE cc_start: 0.7631 (t80) cc_final: 0.7317 (t80) REVERT: B 76 LEU cc_start: 0.8467 (mp) cc_final: 0.8251 (tt) REVERT: B 209 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7213 (tp) REVERT: B 219 GLN cc_start: 0.8141 (tm130) cc_final: 0.7712 (tt0) REVERT: B 332 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7592 (ptt-90) REVERT: B 338 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7239 (mt-10) outliers start: 31 outliers final: 17 residues processed: 126 average time/residue: 0.0955 time to fit residues: 15.1527 Evaluate side-chains 123 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 192 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 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 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 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 47 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.171248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.146141 restraints weight = 10443.587| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.75 r_work: 0.3840 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6212 Z= 0.136 Angle : 0.645 12.347 8455 Z= 0.303 Chirality : 0.042 0.354 945 Planarity : 0.003 0.025 1064 Dihedral : 9.526 86.025 973 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.32 % Allowed : 18.97 % Favored : 75.71 % 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 aren not related in a simple way. whole: 1.51 (0.32), residues: 753 helix: 1.99 (0.23), residues: 514 sheet: 1.32 (0.64), residues: 54 loop : -2.04 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 391 TYR 0.006 0.001 TYR A 244 PHE 0.011 0.001 PHE B 207 TRP 0.007 0.001 TRP B 61 HIS 0.001 0.000 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6212) covalent geometry : angle 0.64529 ( 8455) hydrogen bonds : bond 0.04548 ( 424) hydrogen bonds : angle 4.30377 ( 1263) *********************** 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 139 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7186 (pm20) cc_final: 0.6973 (pm20) REVERT: A 46 SER cc_start: 0.8249 (p) cc_final: 0.7796 (p) REVERT: A 85 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6084 (tp) REVERT: A 185 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6359 (tm-30) REVERT: A 218 GLU cc_start: 0.7273 (tt0) cc_final: 0.7000 (tt0) REVERT: A 228 MET cc_start: 0.8033 (ttm) cc_final: 0.7677 (ttm) REVERT: B 209 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7308 (tp) REVERT: B 332 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7416 (ptt-90) outliers start: 32 outliers final: 20 residues processed: 129 average time/residue: 0.0883 time to fit residues: 14.3916 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 : 0.232 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain A residue 192 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 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 332 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.166576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141808 restraints weight = 10708.060| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.76 r_work: 0.3791 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3004 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= 0.189 Angle : 0.713 14.193 8455 Z= 0.335 Chirality : 0.044 0.373 945 Planarity : 0.004 0.039 1064 Dihedral : 9.896 87.900 973 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.99 % Allowed : 20.13 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.31), residues: 753 helix: 1.78 (0.23), residues: 514 sheet: 1.27 (0.64), residues: 58 loop : -2.17 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 334 TYR 0.008 0.001 TYR A 244 PHE 0.012 0.002 PHE B 207 TRP 0.012 0.001 TRP B 99 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6212) covalent geometry : angle 0.71264 ( 8455) hydrogen bonds : bond 0.05234 ( 424) hydrogen bonds : angle 4.46900 ( 1263) *********************** 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 150 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8288 (p) cc_final: 0.7864 (p) REVERT: A 85 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.5946 (tp) REVERT: A 185 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: A 228 MET cc_start: 0.8079 (ttm) cc_final: 0.7701 (ttm) REVERT: A 334 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7624 (ttm170) REVERT: B 70 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8108 (ttp) REVERT: B 209 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7271 (tp) REVERT: B 290 GLN cc_start: 0.7338 (mp10) cc_final: 0.7041 (mp10) REVERT: B 383 LYS cc_start: 0.8375 (tptp) cc_final: 0.7567 (mmmt) outliers start: 36 outliers final: 21 residues processed: 132 average time/residue: 0.1038 time to fit residues: 16.9073 Evaluate side-chains 132 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 203 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 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 70 MET Chi-restraints excluded: chain B residue 74 ILE 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 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 272 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 chunk 13 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.169394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145743 restraints weight = 10444.954| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.75 r_work: 0.3810 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3194 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= 0.145 Angle : 0.687 14.004 8455 Z= 0.323 Chirality : 0.044 0.404 945 Planarity : 0.003 0.031 1064 Dihedral : 9.694 89.088 973 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.16 % Allowed : 21.63 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.31), residues: 753 helix: 1.95 (0.23), residues: 509 sheet: 1.20 (0.64), residues: 59 loop : -2.13 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.010 0.001 TYR A 319 PHE 0.009 0.001 PHE B 207 TRP 0.009 0.001 TRP B 99 HIS 0.001 0.000 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6212) covalent geometry : angle 0.68741 ( 8455) hydrogen bonds : bond 0.04627 ( 424) hydrogen bonds : angle 4.37145 ( 1263) *********************** 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 141 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7361 (pm20) cc_final: 0.7106 (pm20) REVERT: A 46 SER cc_start: 0.8264 (p) cc_final: 0.7845 (p) REVERT: A 85 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.5887 (tp) REVERT: A 185 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6375 (tm-30) REVERT: A 228 MET cc_start: 0.8031 (ttm) cc_final: 0.7677 (ttm) REVERT: A 235 LEU cc_start: 0.8792 (tt) cc_final: 0.8545 (tt) REVERT: B 209 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7203 (tp) REVERT: B 218 GLU cc_start: 0.7492 (tt0) cc_final: 0.7021 (tt0) REVERT: B 290 GLN cc_start: 0.7381 (mp10) cc_final: 0.7029 (mp10) REVERT: B 334 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7440 (ttp80) REVERT: B 383 LYS cc_start: 0.8314 (tptp) cc_final: 0.7521 (mmmt) outliers start: 31 outliers final: 23 residues processed: 128 average time/residue: 0.0993 time to fit residues: 15.8236 Evaluate side-chains 133 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 192 LEU 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 272 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 47 optimal weight: 0.0980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.170199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.146479 restraints weight = 10452.043| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.72 r_work: 0.3835 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6212 Z= 0.136 Angle : 0.687 11.634 8455 Z= 0.320 Chirality : 0.043 0.404 945 Planarity : 0.003 0.037 1064 Dihedral : 9.499 87.216 973 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.83 % Allowed : 22.63 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.32), residues: 753 helix: 2.02 (0.23), residues: 519 sheet: 1.22 (0.65), residues: 59 loop : -2.36 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 334 TYR 0.008 0.001 TYR A 244 PHE 0.008 0.001 PHE B 182 TRP 0.010 0.001 TRP B 61 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6212) covalent geometry : angle 0.68700 ( 8455) hydrogen bonds : bond 0.04419 ( 424) hydrogen bonds : angle 4.33199 ( 1263) *********************** 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 143 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8238 (p) cc_final: 0.7830 (p) REVERT: A 85 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.5910 (tp) REVERT: A 185 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 228 MET cc_start: 0.8008 (ttm) cc_final: 0.7663 (ttm) REVERT: A 235 LEU cc_start: 0.8816 (tt) cc_final: 0.8582 (tt) REVERT: A 288 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7851 (mm) REVERT: A 377 ARG cc_start: 0.8041 (tpm-80) cc_final: 0.7744 (tpm-80) REVERT: B 209 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7241 (tp) REVERT: B 218 GLU cc_start: 0.7427 (tt0) cc_final: 0.7092 (tt0) REVERT: B 290 GLN cc_start: 0.7345 (mp10) cc_final: 0.6987 (mp10) REVERT: B 332 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7349 (ptt-90) REVERT: B 383 LYS cc_start: 0.8318 (tptp) cc_final: 0.7581 (mmmt) outliers start: 29 outliers final: 22 residues processed: 133 average time/residue: 0.0966 time to fit residues: 15.8366 Evaluate side-chains 137 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 203 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 288 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 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 203 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 332 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.169157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144954 restraints weight = 10416.261| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.71 r_work: 0.3842 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3441 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= 0.142 Angle : 0.688 12.118 8455 Z= 0.327 Chirality : 0.043 0.395 945 Planarity : 0.004 0.107 1064 Dihedral : 9.419 85.742 973 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.32 % Allowed : 23.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.32), residues: 753 helix: 2.04 (0.23), residues: 520 sheet: 1.29 (0.65), residues: 59 loop : -2.32 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 391 TYR 0.009 0.001 TYR A 244 PHE 0.009 0.001 PHE B 41 TRP 0.009 0.001 TRP B 61 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6212) covalent geometry : angle 0.68836 ( 8455) hydrogen bonds : bond 0.04428 ( 424) hydrogen bonds : angle 4.33373 ( 1263) *********************** 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 141 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8246 (p) cc_final: 0.7848 (p) REVERT: A 85 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6057 (tp) REVERT: A 185 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6318 (tm-30) REVERT: A 288 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 377 ARG cc_start: 0.8071 (tpm-80) cc_final: 0.7745 (tpm-80) REVERT: B 41 PHE cc_start: 0.7701 (t80) cc_final: 0.7397 (t80) REVERT: B 218 GLU cc_start: 0.7427 (tt0) cc_final: 0.6869 (tt0) REVERT: B 290 GLN cc_start: 0.7411 (mp10) cc_final: 0.7015 (mp10) REVERT: B 332 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7364 (ptt-90) REVERT: B 383 LYS cc_start: 0.8317 (tptp) cc_final: 0.7536 (mmmt) outliers start: 32 outliers final: 24 residues processed: 130 average time/residue: 0.0948 time to fit residues: 15.4002 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 : 0.130 ------------------------------------------------------------------------------- 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 192 LEU 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 63 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 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 203 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 329 ILE 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 61 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 44 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.168908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144778 restraints weight = 10360.601| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.65 r_work: 0.3847 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6212 Z= 0.143 Angle : 0.711 12.438 8455 Z= 0.337 Chirality : 0.043 0.392 945 Planarity : 0.006 0.160 1064 Dihedral : 9.347 84.120 973 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.99 % Allowed : 23.79 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.32), residues: 753 helix: 2.03 (0.23), residues: 520 sheet: 1.24 (0.64), residues: 59 loop : -2.38 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 334 TYR 0.009 0.001 TYR A 244 PHE 0.008 0.001 PHE B 207 TRP 0.010 0.001 TRP B 61 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6212) covalent geometry : angle 0.71128 ( 8455) hydrogen bonds : bond 0.04405 ( 424) hydrogen bonds : angle 4.32149 ( 1263) *********************** 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: 30 poor density : 104 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8238 (p) cc_final: 0.7839 (p) REVERT: A 85 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6071 (tp) REVERT: A 185 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6277 (tm-30) REVERT: A 288 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7847 (mm) REVERT: A 377 ARG cc_start: 0.8036 (tpm-80) cc_final: 0.7708 (tpm-80) REVERT: B 218 GLU cc_start: 0.7302 (tt0) cc_final: 0.7010 (tt0) REVERT: B 290 GLN cc_start: 0.7467 (mp10) cc_final: 0.7049 (mp10) REVERT: B 332 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7421 (ptt-90) REVERT: B 383 LYS cc_start: 0.8250 (tptp) cc_final: 0.7489 (mmmt) outliers start: 30 outliers final: 24 residues processed: 125 average time/residue: 0.1010 time to fit residues: 15.6171 Evaluate side-chains 131 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 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 110 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 188 LEU Chi-restraints excluded: chain B residue 203 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 332 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.171041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.147109 restraints weight = 10275.564| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.68 r_work: 0.3851 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6212 Z= 0.135 Angle : 0.700 12.601 8455 Z= 0.331 Chirality : 0.043 0.380 945 Planarity : 0.004 0.099 1064 Dihedral : 9.213 85.554 973 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.66 % Allowed : 24.13 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.32), residues: 753 helix: 2.06 (0.23), residues: 520 sheet: 1.21 (0.64), residues: 59 loop : -2.42 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 391 TYR 0.009 0.001 TYR A 244 PHE 0.008 0.001 PHE A 41 TRP 0.010 0.001 TRP B 61 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6212) covalent geometry : angle 0.70046 ( 8455) hydrogen bonds : bond 0.04251 ( 424) hydrogen bonds : angle 4.29240 ( 1263) ********************** 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 133 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8221 (p) cc_final: 0.7823 (p) REVERT: A 85 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6112 (tp) REVERT: A 185 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: A 288 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 377 ARG cc_start: 0.7997 (tpm-80) cc_final: 0.7670 (tpm-80) REVERT: B 218 GLU cc_start: 0.7272 (tt0) cc_final: 0.6988 (tt0) REVERT: B 290 GLN cc_start: 0.7447 (mp10) cc_final: 0.7047 (mp10) REVERT: B 308 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6608 (ptm160) REVERT: B 332 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7442 (ptt-90) REVERT: B 383 LYS cc_start: 0.8213 (tptp) cc_final: 0.7458 (mmmt) outliers start: 28 outliers final: 21 residues processed: 125 average time/residue: 0.1042 time to fit residues: 16.2025 Evaluate side-chains 133 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 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 110 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 203 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE 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 27 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 0.0770 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.168066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.143587 restraints weight = 10359.812| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.68 r_work: 0.3813 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3668 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= 0.158 Angle : 0.718 12.517 8455 Z= 0.342 Chirality : 0.044 0.389 945 Planarity : 0.004 0.078 1064 Dihedral : 9.288 86.163 973 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.66 % Allowed : 24.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.31), residues: 753 helix: 1.95 (0.23), residues: 520 sheet: 1.23 (0.64), residues: 59 loop : -2.49 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 242 TYR 0.010 0.001 TYR A 244 PHE 0.009 0.001 PHE B 207 TRP 0.008 0.001 TRP B 99 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6212) covalent geometry : angle 0.71758 ( 8455) hydrogen bonds : bond 0.04625 ( 424) hydrogen bonds : angle 4.37033 ( 1263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.22 seconds wall clock time: 24 minutes 50.32 seconds (1490.32 seconds total)