Starting phenix.real_space_refine on Fri Jul 19 03:06:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/07_2024/8wcn_37444_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/07_2024/8wcn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/07_2024/8wcn_37444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/07_2024/8wcn_37444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/07_2024/8wcn_37444_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/07_2024/8wcn_37444_neut.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 Residue "A GLU 313": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.85, per 1000 atoms: 0.80 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 - 3.50 Amino acid : False - 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: 2.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.51 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: 1.60 Time building geometry restraints manager: 2.68 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: 98.13 - 105.29: 112 105.29 - 112.46: 3079 112.46 - 119.62: 2119 119.62 - 126.78: 3049 126.78 - 133.95: 96 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 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: 0.000 Normalize map: mean=0, sd=1: 3.260 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.640 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- 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= 0.232 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.614 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: 0.2678 time to fit residues: 40.2687 Evaluate side-chains 110 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 B 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6212 Z= 0.321 Angle : 0.689 7.852 8455 Z= 0.344 Chirality : 0.046 0.376 945 Planarity : 0.004 0.032 1064 Dihedral : 10.783 76.250 973 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.49 % Allowed : 16.97 % Favored : 77.54 % 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: 1.03 (0.31), residues: 753 helix: 1.46 (0.23), residues: 514 sheet: 1.71 (0.60), residues: 59 loop : -2.00 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS A 136 PHE 0.017 0.002 PHE B 207 TYR 0.008 0.001 TYR A 244 ARG 0.005 0.001 ARG B 377 *********************** 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 141 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7191 (pm20) cc_final: 0.6951 (pm20) REVERT: A 228 MET cc_start: 0.7085 (ttm) cc_final: 0.6645 (ttm) REVERT: A 303 LEU cc_start: 0.8047 (mt) cc_final: 0.7638 (tt) REVERT: A 313 GLU cc_start: 0.6569 (pp20) cc_final: 0.6361 (pp20) REVERT: A 338 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 377 ARG cc_start: 0.8517 (tpm-80) cc_final: 0.8107 (tpm-80) REVERT: B 41 PHE cc_start: 0.7111 (t80) cc_final: 0.6787 (t80) REVERT: B 76 LEU cc_start: 0.8780 (mp) cc_final: 0.8406 (tt) REVERT: B 278 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7320 (m-70) REVERT: B 334 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7916 (ttp80) REVERT: B 338 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8244 (mt-10) REVERT: B 343 GLU cc_start: 0.7470 (pm20) cc_final: 0.7241 (pm20) outliers start: 33 outliers final: 20 residues processed: 128 average time/residue: 0.2296 time to fit residues: 36.6584 Evaluate side-chains 120 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 46 SER 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 219 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6212 Z= 0.183 Angle : 0.639 10.945 8455 Z= 0.302 Chirality : 0.042 0.311 945 Planarity : 0.003 0.021 1064 Dihedral : 9.728 81.862 973 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.32 % Allowed : 20.13 % Favored : 74.54 % 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: 1.17 (0.31), residues: 753 helix: 1.66 (0.23), residues: 515 sheet: 1.53 (0.64), residues: 54 loop : -2.11 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.001 0.000 HIS B 136 PHE 0.022 0.001 PHE A 81 TYR 0.005 0.001 TYR A 319 ARG 0.004 0.000 ARG A 391 *********************** 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 142 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7247 (pm20) cc_final: 0.7020 (pm20) REVERT: A 46 SER cc_start: 0.7671 (p) cc_final: 0.7183 (p) REVERT: A 185 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6611 (tm-30) REVERT: A 218 GLU cc_start: 0.7251 (tt0) cc_final: 0.6596 (tt0) REVERT: A 228 MET cc_start: 0.7122 (ttm) cc_final: 0.6627 (ttm) REVERT: A 313 GLU cc_start: 0.6626 (pp20) cc_final: 0.6368 (pp20) REVERT: A 338 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 377 ARG cc_start: 0.8491 (tpm-80) cc_final: 0.8077 (tpm-80) REVERT: B 41 PHE cc_start: 0.6936 (t80) cc_final: 0.6623 (t80) REVERT: B 46 SER cc_start: 0.6793 (OUTLIER) cc_final: 0.6488 (m) REVERT: B 70 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7987 (ttp) REVERT: B 278 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7260 (m-70) REVERT: B 290 GLN cc_start: 0.7822 (mp10) cc_final: 0.7418 (mp10) REVERT: B 305 ILE cc_start: 0.4812 (OUTLIER) cc_final: 0.4489 (pt) REVERT: B 332 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8366 (ptt-90) REVERT: B 334 ARG cc_start: 0.8382 (ttp80) cc_final: 0.7859 (ttp80) REVERT: B 338 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 391 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.7191 (mmt-90) outliers start: 32 outliers final: 17 residues processed: 133 average time/residue: 0.2204 time to fit residues: 36.4204 Evaluate side-chains 128 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL 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 46 SER Chi-restraints excluded: chain B residue 70 MET 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 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 219 GLN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 305 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 66 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.0570 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2727 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= 0.176 Angle : 0.607 10.908 8455 Z= 0.292 Chirality : 0.042 0.368 945 Planarity : 0.003 0.021 1064 Dihedral : 9.389 83.329 973 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.66 % Allowed : 21.80 % Favored : 73.54 % 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: 1.35 (0.31), residues: 753 helix: 1.85 (0.23), residues: 515 sheet: 1.41 (0.64), residues: 54 loop : -2.14 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.001 0.000 HIS B 136 PHE 0.020 0.001 PHE A 81 TYR 0.006 0.001 TYR A 244 ARG 0.005 0.000 ARG A 391 *********************** 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 138 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7322 (pm20) cc_final: 0.7096 (pm20) REVERT: A 46 SER cc_start: 0.7648 (p) cc_final: 0.7178 (p) REVERT: A 185 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: A 228 MET cc_start: 0.7147 (ttm) cc_final: 0.6627 (ttm) REVERT: A 303 LEU cc_start: 0.7570 (mp) cc_final: 0.7147 (tt) REVERT: A 313 GLU cc_start: 0.6664 (pp20) cc_final: 0.6371 (pp20) REVERT: A 334 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8245 (ttm170) REVERT: A 338 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 377 ARG cc_start: 0.8484 (tpm-80) cc_final: 0.8109 (tpm-80) REVERT: B 278 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.7255 (m-70) REVERT: B 290 GLN cc_start: 0.7874 (mp10) cc_final: 0.7433 (mp10) REVERT: B 305 ILE cc_start: 0.4815 (OUTLIER) cc_final: 0.4585 (pt) REVERT: B 332 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8316 (ptt-90) REVERT: B 334 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8133 (ttm170) REVERT: B 338 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8272 (mt-10) REVERT: B 381 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8623 (tm-30) REVERT: B 383 LYS cc_start: 0.8339 (tptp) cc_final: 0.7154 (mmmt) REVERT: B 391 ARG cc_start: 0.7596 (mmt-90) cc_final: 0.7296 (mmt-90) outliers start: 28 outliers final: 19 residues processed: 128 average time/residue: 0.2304 time to fit residues: 36.9325 Evaluate side-chains 132 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 238 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 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 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 305 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 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 1 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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 ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6212 Z= 0.163 Angle : 0.607 11.221 8455 Z= 0.286 Chirality : 0.041 0.359 945 Planarity : 0.003 0.020 1064 Dihedral : 9.214 84.835 973 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.49 % Allowed : 23.96 % Favored : 71.55 % 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: 1.54 (0.32), residues: 753 helix: 2.02 (0.23), residues: 515 sheet: 1.40 (0.64), residues: 54 loop : -2.15 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.001 0.000 HIS B 136 PHE 0.017 0.001 PHE A 81 TYR 0.007 0.001 TYR A 244 ARG 0.004 0.000 ARG B 242 *********************** 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 136 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7340 (pm20) cc_final: 0.7116 (pm20) REVERT: A 46 SER cc_start: 0.7648 (p) cc_final: 0.7190 (p) REVERT: A 185 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: A 313 GLU cc_start: 0.6698 (pp20) cc_final: 0.6379 (pp20) REVERT: A 331 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8952 (mm-30) REVERT: A 334 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8135 (ttm170) REVERT: A 338 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8274 (mt-10) REVERT: B 278 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.7233 (m-70) REVERT: B 290 GLN cc_start: 0.7907 (mp10) cc_final: 0.7439 (mp10) REVERT: B 305 ILE cc_start: 0.4764 (OUTLIER) cc_final: 0.4473 (pt) REVERT: B 322 GLU cc_start: 0.8235 (pm20) cc_final: 0.7544 (pp20) REVERT: B 334 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8148 (ttm170) REVERT: B 338 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 383 LYS cc_start: 0.8239 (tptp) cc_final: 0.7101 (mmmt) outliers start: 27 outliers final: 18 residues processed: 130 average time/residue: 0.2284 time to fit residues: 37.3183 Evaluate side-chains 128 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 70 MET 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 175 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU 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 305 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6212 Z= 0.225 Angle : 0.618 11.381 8455 Z= 0.298 Chirality : 0.043 0.372 945 Planarity : 0.003 0.026 1064 Dihedral : 9.363 85.260 973 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.16 % Allowed : 23.13 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.31), residues: 753 helix: 1.98 (0.23), residues: 510 sheet: 1.67 (0.61), residues: 63 loop : -2.33 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.002 0.000 HIS A 136 PHE 0.013 0.002 PHE B 207 TYR 0.007 0.001 TYR A 244 ARG 0.006 0.000 ARG B 242 *********************** 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 147 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7692 (p) cc_final: 0.7219 (p) REVERT: A 185 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: A 235 LEU cc_start: 0.8910 (tt) cc_final: 0.8512 (tt) REVERT: A 278 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7637 (m-70) REVERT: A 313 GLU cc_start: 0.6712 (pp20) cc_final: 0.5864 (pp20) REVERT: A 331 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8926 (mm-30) REVERT: A 334 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8343 (ptm160) REVERT: A 338 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 278 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7253 (m-70) REVERT: B 290 GLN cc_start: 0.8004 (mp10) cc_final: 0.7531 (mp10) REVERT: B 305 ILE cc_start: 0.4789 (OUTLIER) cc_final: 0.4550 (pt) REVERT: B 332 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8284 (ptt-90) REVERT: B 334 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8179 (ttm170) REVERT: B 338 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 391 ARG cc_start: 0.7813 (mmt-90) cc_final: 0.7568 (mmt-90) outliers start: 31 outliers final: 22 residues processed: 136 average time/residue: 0.2390 time to fit residues: 40.3074 Evaluate side-chains 140 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 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 175 ASN 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 Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 305 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 69 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3261 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= 0.217 Angle : 0.634 10.915 8455 Z= 0.301 Chirality : 0.043 0.385 945 Planarity : 0.003 0.029 1064 Dihedral : 9.316 86.844 973 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.49 % Allowed : 24.29 % Favored : 70.22 % 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: 1.48 (0.31), residues: 753 helix: 2.00 (0.23), residues: 510 sheet: 1.44 (0.60), residues: 67 loop : -2.45 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.000 HIS A 136 PHE 0.013 0.002 PHE A 81 TYR 0.008 0.001 TYR A 244 ARG 0.006 0.000 ARG B 242 *********************** 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 152 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7687 (p) cc_final: 0.7222 (p) REVERT: A 185 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: A 192 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7449 (mt) REVERT: A 235 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 278 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7652 (m-70) REVERT: A 313 GLU cc_start: 0.6756 (pp20) cc_final: 0.6028 (pp20) REVERT: A 331 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8890 (mm-30) REVERT: A 334 ARG cc_start: 0.8886 (ttp80) cc_final: 0.7884 (ptm160) REVERT: A 338 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 377 ARG cc_start: 0.8483 (tpm-80) cc_final: 0.8141 (tpm-80) REVERT: B 278 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7274 (m-70) REVERT: B 290 GLN cc_start: 0.8030 (mp10) cc_final: 0.7541 (mp10) REVERT: B 305 ILE cc_start: 0.4760 (OUTLIER) cc_final: 0.4520 (pt) REVERT: B 332 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8252 (ptt-90) REVERT: B 334 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8260 (ttm170) REVERT: B 338 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 383 LYS cc_start: 0.8171 (tptp) cc_final: 0.7024 (mmmt) REVERT: B 391 ARG cc_start: 0.7795 (mmt-90) cc_final: 0.7435 (mmt180) outliers start: 33 outliers final: 24 residues processed: 140 average time/residue: 0.2278 time to fit residues: 39.6395 Evaluate side-chains 153 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 218 GLU Chi-restraints excluded: chain A residue 235 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 278 HIS 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 175 ASN 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 247 LEU 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 305 ILE Chi-restraints excluded: chain B residue 329 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 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.0020 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.5366 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3387 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= 0.199 Angle : 0.622 11.426 8455 Z= 0.298 Chirality : 0.042 0.373 945 Planarity : 0.003 0.029 1064 Dihedral : 9.209 88.005 973 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.99 % Allowed : 24.46 % 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: 1.51 (0.31), residues: 753 helix: 2.03 (0.23), residues: 511 sheet: 1.38 (0.59), residues: 67 loop : -2.44 (0.42), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.001 0.000 HIS A 136 PHE 0.013 0.001 PHE A 81 TYR 0.009 0.001 TYR A 244 ARG 0.006 0.000 ARG B 242 *********************** 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 155 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7685 (p) cc_final: 0.7229 (p) REVERT: A 185 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: A 192 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7434 (mt) REVERT: A 235 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8507 (tt) REVERT: A 272 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: A 313 GLU cc_start: 0.6944 (pp20) cc_final: 0.6576 (pp20) REVERT: A 331 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8890 (mm-30) REVERT: A 334 ARG cc_start: 0.8900 (ttp80) cc_final: 0.7964 (ptm160) REVERT: A 338 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 377 ARG cc_start: 0.8464 (tpm-80) cc_final: 0.8110 (tpm-80) REVERT: B 278 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7283 (m-70) REVERT: B 290 GLN cc_start: 0.8043 (mp10) cc_final: 0.7546 (mp10) REVERT: B 305 ILE cc_start: 0.4734 (OUTLIER) cc_final: 0.4429 (pt) REVERT: B 332 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8203 (ptt-90) REVERT: B 338 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 383 LYS cc_start: 0.8132 (tptp) cc_final: 0.6980 (mmmt) REVERT: B 391 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.7499 (mmp80) outliers start: 36 outliers final: 24 residues processed: 143 average time/residue: 0.2171 time to fit residues: 38.8247 Evaluate side-chains 149 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 218 GLU Chi-restraints excluded: chain A residue 235 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 272 PHE 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 110 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 229 MET Chi-restraints excluded: chain B residue 247 LEU 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 305 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 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.0010 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3508 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= 0.179 Angle : 0.641 11.192 8455 Z= 0.299 Chirality : 0.042 0.404 945 Planarity : 0.003 0.029 1064 Dihedral : 9.067 89.280 973 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.32 % Allowed : 24.96 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.31), residues: 753 helix: 2.05 (0.23), residues: 515 sheet: 1.54 (0.61), residues: 63 loop : -2.42 (0.42), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.001 0.000 HIS B 344 PHE 0.013 0.001 PHE A 81 TYR 0.010 0.001 TYR A 244 ARG 0.007 0.000 ARG B 242 *********************** 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 147 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7692 (p) cc_final: 0.7249 (p) REVERT: A 185 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: A 235 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 272 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: A 278 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7600 (m-70) REVERT: A 313 GLU cc_start: 0.6927 (pp20) cc_final: 0.6561 (pp20) REVERT: A 331 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8846 (mm-30) REVERT: A 334 ARG cc_start: 0.8858 (ttp80) cc_final: 0.7824 (ptm160) REVERT: A 338 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 377 ARG cc_start: 0.8478 (tpm-80) cc_final: 0.8118 (tpm-80) REVERT: B 278 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7288 (m-70) REVERT: B 290 GLN cc_start: 0.8034 (mp10) cc_final: 0.7529 (mp10) REVERT: B 305 ILE cc_start: 0.4726 (OUTLIER) cc_final: 0.4484 (pt) REVERT: B 332 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8139 (ptt-90) REVERT: B 338 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8347 (mt-10) REVERT: B 383 LYS cc_start: 0.8110 (tptp) cc_final: 0.6969 (mmmt) outliers start: 32 outliers final: 20 residues processed: 139 average time/residue: 0.2263 time to fit residues: 39.1715 Evaluate side-chains 142 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 218 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 278 HIS 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 110 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 265 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 305 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 33 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3560 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= 0.203 Angle : 0.638 11.244 8455 Z= 0.304 Chirality : 0.043 0.408 945 Planarity : 0.003 0.031 1064 Dihedral : 9.093 89.692 973 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.83 % Allowed : 25.79 % 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: 1.49 (0.31), residues: 753 helix: 2.00 (0.23), residues: 515 sheet: 1.52 (0.61), residues: 63 loop : -2.47 (0.42), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.002 0.000 HIS B 344 PHE 0.016 0.002 PHE A 81 TYR 0.009 0.001 TYR A 244 ARG 0.007 0.000 ARG B 242 ********************** 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 143 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7703 (p) cc_final: 0.7252 (p) REVERT: A 185 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: A 235 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8142 (tt) REVERT: A 278 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7569 (m-70) REVERT: A 313 GLU cc_start: 0.6917 (pp20) cc_final: 0.6549 (pp20) REVERT: A 334 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8242 (ttp-170) REVERT: A 338 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8089 (mt-10) REVERT: A 377 ARG cc_start: 0.8495 (tpm-80) cc_final: 0.8133 (tpm-80) REVERT: B 278 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7313 (m-70) REVERT: B 290 GLN cc_start: 0.8052 (mp10) cc_final: 0.7552 (mp10) REVERT: B 305 ILE cc_start: 0.4746 (OUTLIER) cc_final: 0.4505 (pt) REVERT: B 322 GLU cc_start: 0.8307 (pm20) cc_final: 0.7775 (pp20) REVERT: B 332 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8140 (ptt-90) REVERT: B 338 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 343 GLU cc_start: 0.7755 (pm20) cc_final: 0.7373 (pm20) REVERT: B 383 LYS cc_start: 0.8117 (tptp) cc_final: 0.6981 (mmmt) REVERT: B 391 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.7258 (mmt-90) outliers start: 29 outliers final: 22 residues processed: 135 average time/residue: 0.2327 time to fit residues: 38.8568 Evaluate side-chains 142 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 218 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 278 HIS 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 110 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 247 LEU 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 305 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 54 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.164178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.139377 restraints weight = 10195.734| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.61 r_work: 0.3795 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6212 Z= 0.234 Angle : 0.668 11.298 8455 Z= 0.320 Chirality : 0.044 0.408 945 Planarity : 0.003 0.022 1064 Dihedral : 9.152 89.872 973 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.32 % Allowed : 26.12 % Favored : 68.55 % 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: 511 sheet: 1.30 (0.61), residues: 64 loop : -2.39 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS A 136 PHE 0.017 0.002 PHE A 81 TYR 0.009 0.001 TYR A 244 ARG 0.006 0.000 ARG A 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.28 seconds wall clock time: 32 minutes 5.40 seconds (1925.40 seconds total)