Starting phenix.real_space_refine on Fri Apr 5 22:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/04_2024/8wcn_37444_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/04_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_37444/04_2024/8wcn_37444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/04_2024/8wcn_37444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/04_2024/8wcn_37444_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcn_37444/04_2024/8wcn_37444_updated.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.71, per 1000 atoms: 0.61 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 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... running ksdssp... Secondary structure from input PDB file: 27 helices and 2 sheets defined 65.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 47 through 71 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 78 through 101 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 105 through 111 removed outlier: 5.681A pdb=" N LYS A 109 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 135 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 143 through 151 removed outlier: 3.670A pdb=" N ALA A 146 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 151 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 181 Processing helix chain 'A' and resid 188 through 231 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 241 through 258 Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.522A pdb=" N GLN A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'B' and resid 16 through 23 Processing helix chain 'B' and resid 32 through 45 Processing helix chain 'B' and resid 47 through 71 Processing helix chain 'B' and resid 78 through 103 Proline residue: B 100 - end of helix removed outlier: 3.795A pdb=" N PHE B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 133 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) removed outlier: 3.590A pdb=" N ILE B 114 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 115 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Proline residue: B 116 - end of helix removed outlier: 3.944A pdb=" N LEU B 120 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 121 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS B 129 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 161 through 180 removed outlier: 3.853A pdb=" N PHE B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 231 removed outlier: 3.693A pdb=" N ALA B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 281 through 297 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) removed outlier: 5.295A pdb=" N LEU B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 340 Processing helix chain 'B' and resid 368 through 383 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= A, first strand: chain 'A' and resid 355 through 362 removed outlier: 3.593A pdb=" N VAL A 262 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 310 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA A 315 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG A 308 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU A 317 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ALA A 306 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 355 through 362 386 hydrogen bonds defined for protein. 1083 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: 1.67 Time building geometry restraints manager: 2.48 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: 40 2.50 - 3.10: 4402 3.10 - 3.70: 9789 3.70 - 4.30: 12976 4.30 - 4.90: 20630 Nonbonded interactions: 47837 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 47832 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: 6.540 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: 9.400 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.410 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- 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= 0.228 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 : 0.651 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: 0.2597 time to fit residues: 38.4601 Evaluate side-chains 110 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.0050 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 overall best weight: 0.4172 ------------------------------------------------------------------------------- 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: 0.6823 moved from start: 0.1685 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= 0.184 Angle : 0.614 8.443 8455 Z= 0.296 Chirality : 0.041 0.333 945 Planarity : 0.003 0.022 1064 Dihedral : 10.349 78.119 973 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.00 % Allowed : 18.97 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.32), residues: 753 helix: 1.74 (0.24), residues: 519 sheet: 1.81 (0.58), residues: 59 loop : -1.84 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.001 HIS B 136 PHE 0.012 0.001 PHE B 207 TYR 0.007 0.001 TYR A 244 ARG 0.010 0.001 ARG B 334 *********************** 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 125 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7583 (t0) cc_final: 0.7232 (t0) REVERT: A 85 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5120 (tt) REVERT: A 186 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 303 LEU cc_start: 0.7972 (mt) cc_final: 0.7634 (tt) REVERT: A 313 GLU cc_start: 0.6434 (pp20) cc_final: 0.6203 (pp20) REVERT: A 322 GLU cc_start: 0.8217 (pm20) cc_final: 0.7949 (pm20) REVERT: A 334 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8182 (ttm170) REVERT: A 338 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 377 ARG cc_start: 0.8496 (tpm-80) cc_final: 0.8052 (tpm-80) REVERT: A 383 LYS cc_start: 0.7625 (tppt) cc_final: 0.7356 (tptt) REVERT: B 41 PHE cc_start: 0.7059 (t80) cc_final: 0.6698 (t80) REVERT: B 63 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6234 (tp) REVERT: B 70 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7955 (ttp) REVERT: B 180 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7391 (mt) REVERT: B 305 ILE cc_start: 0.4821 (OUTLIER) cc_final: 0.4604 (pt) REVERT: B 334 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7836 (ttp80) REVERT: B 338 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 366 MET cc_start: 0.6867 (tmm) cc_final: 0.6622 (tmm) REVERT: B 391 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.7172 (mmt180) outliers start: 18 outliers final: 9 residues processed: 117 average time/residue: 0.2314 time to fit residues: 33.5193 Evaluate side-chains 111 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 305 ILE Chi-restraints excluded: chain B residue 368 LEU 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: 0.8980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 0.0020 chunk 54 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2264 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= 0.198 Angle : 0.594 10.734 8455 Z= 0.285 Chirality : 0.041 0.309 945 Planarity : 0.003 0.024 1064 Dihedral : 9.537 81.025 973 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.99 % Allowed : 19.30 % 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 (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 (0.32), residues: 753 helix: 1.76 (0.24), residues: 523 sheet: 1.60 (0.60), residues: 54 loop : -2.04 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.001 0.001 HIS A 77 PHE 0.012 0.001 PHE B 207 TYR 0.007 0.001 TYR A 244 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 137 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7712 (p) cc_final: 0.7305 (p) REVERT: A 85 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5347 (tp) REVERT: A 91 MET cc_start: 0.4761 (mmp) cc_final: 0.4560 (mmp) REVERT: A 185 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6652 (tm-30) REVERT: A 303 LEU cc_start: 0.7933 (mt) cc_final: 0.7609 (tt) REVERT: A 313 GLU cc_start: 0.6462 (pp20) cc_final: 0.6249 (pp20) REVERT: A 338 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8215 (mt-10) REVERT: A 377 ARG cc_start: 0.8478 (tpm-80) cc_final: 0.8075 (tpm-80) REVERT: A 383 LYS cc_start: 0.7544 (tppt) cc_final: 0.7258 (tptt) REVERT: B 63 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6240 (tp) REVERT: B 235 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8523 (tt) REVERT: B 290 GLN cc_start: 0.7830 (mp10) cc_final: 0.7413 (mp10) REVERT: B 327 LEU cc_start: 0.9165 (mm) cc_final: 0.8893 (mm) REVERT: B 332 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8359 (ptt-90) REVERT: B 334 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7896 (ttp80) REVERT: B 338 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 391 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.7401 (mmp80) outliers start: 30 outliers final: 15 residues processed: 131 average time/residue: 0.2150 time to fit residues: 35.3881 Evaluate side-chains 124 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 278 HIS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 LEU 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 66 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 34 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6212 Z= 0.174 Angle : 0.581 10.575 8455 Z= 0.279 Chirality : 0.041 0.373 945 Planarity : 0.003 0.024 1064 Dihedral : 9.388 82.314 973 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.66 % Allowed : 21.30 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.32), residues: 753 helix: 1.79 (0.24), residues: 523 sheet: 1.41 (0.60), residues: 54 loop : -2.02 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 61 HIS 0.002 0.000 HIS A 344 PHE 0.010 0.001 PHE B 207 TYR 0.014 0.001 TYR A 372 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 134 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7356 (pm20) cc_final: 0.7119 (pm20) REVERT: A 46 SER cc_start: 0.7688 (p) cc_final: 0.7292 (p) REVERT: A 64 PHE cc_start: 0.6056 (m-10) cc_final: 0.5855 (m-10) REVERT: A 85 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5310 (tp) REVERT: A 185 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6436 (tm-30) REVERT: A 186 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 218 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: A 303 LEU cc_start: 0.7646 (mt) cc_final: 0.7437 (tt) REVERT: A 313 GLU cc_start: 0.6471 (pp20) cc_final: 0.6233 (pp20) REVERT: A 334 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8312 (ttm170) REVERT: A 338 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8282 (mt-10) REVERT: A 383 LYS cc_start: 0.7651 (tppt) cc_final: 0.7363 (tptt) REVERT: B 63 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6222 (tp) REVERT: B 290 GLN cc_start: 0.7865 (mp10) cc_final: 0.7424 (mp10) REVERT: B 305 ILE cc_start: 0.4818 (OUTLIER) cc_final: 0.4595 (pt) REVERT: B 327 LEU cc_start: 0.9138 (mm) cc_final: 0.8904 (mm) REVERT: B 334 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8156 (ttm170) REVERT: B 338 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8304 (mt-10) REVERT: B 391 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.7488 (mmp80) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.2407 time to fit residues: 37.5786 Evaluate side-chains 126 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 46 SER 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 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 305 ILE Chi-restraints excluded: chain B residue 368 LEU 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: 0.6980 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 249 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: 0.6891 moved from start: 0.2807 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= 0.235 Angle : 0.604 10.696 8455 Z= 0.292 Chirality : 0.042 0.380 945 Planarity : 0.003 0.023 1064 Dihedral : 9.598 83.996 973 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.16 % Allowed : 21.96 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.31), residues: 753 helix: 1.66 (0.23), residues: 522 sheet: 1.48 (0.56), residues: 63 loop : -2.28 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.000 HIS A 136 PHE 0.013 0.002 PHE B 207 TYR 0.009 0.001 TYR A 372 ARG 0.003 0.000 ARG B 75 *********************** 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 141 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7792 (p) cc_final: 0.7405 (p) REVERT: A 85 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.5184 (tp) REVERT: A 91 MET cc_start: 0.4964 (mmp) cc_final: 0.4755 (mmp) REVERT: A 185 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6625 (tm-30) REVERT: A 218 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: A 313 GLU cc_start: 0.6509 (pp20) cc_final: 0.6226 (pp20) REVERT: A 331 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8998 (mm-30) REVERT: A 334 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8347 (ttm170) REVERT: A 338 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 391 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7960 (mmt-90) REVERT: B 278 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7239 (m-70) REVERT: B 290 GLN cc_start: 0.7995 (mp10) cc_final: 0.7538 (mp10) REVERT: B 305 ILE cc_start: 0.4772 (OUTLIER) cc_final: 0.4545 (pt) REVERT: B 332 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8272 (ptt-90) REVERT: B 334 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7948 (ttp80) REVERT: B 338 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8322 (mt-10) REVERT: B 391 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7609 (mmt180) outliers start: 31 outliers final: 17 residues processed: 133 average time/residue: 0.2421 time to fit residues: 39.8202 Evaluate side-chains 129 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 218 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 46 SER 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 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 Chi-restraints excluded: chain B residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 249 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: 0.6856 moved from start: 0.2949 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= 0.170 Angle : 0.602 11.598 8455 Z= 0.284 Chirality : 0.041 0.353 945 Planarity : 0.003 0.021 1064 Dihedral : 9.369 85.678 973 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.32 % Allowed : 22.80 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.31), residues: 753 helix: 1.70 (0.24), residues: 523 sheet: 1.47 (0.57), residues: 58 loop : -2.31 (0.42), residues: 172 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 0.009 0.001 PHE B 207 TYR 0.009 0.001 TYR A 372 ARG 0.002 0.000 ARG B 75 *********************** 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 144 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7713 (p) cc_final: 0.7344 (p) REVERT: A 85 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5164 (tp) REVERT: A 91 MET cc_start: 0.4914 (mmp) cc_final: 0.4662 (mmp) REVERT: A 185 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: A 186 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 218 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: A 235 LEU cc_start: 0.8823 (tt) cc_final: 0.8368 (tt) REVERT: A 272 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: A 313 GLU cc_start: 0.6500 (pp20) cc_final: 0.6007 (pp20) REVERT: A 331 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9018 (mm-30) REVERT: A 334 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8643 (ttm170) REVERT: A 391 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7932 (mmt-90) REVERT: B 278 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7220 (m-70) REVERT: B 290 GLN cc_start: 0.8017 (mp10) cc_final: 0.7536 (mp10) REVERT: B 305 ILE cc_start: 0.4740 (OUTLIER) cc_final: 0.4443 (pt) REVERT: B 332 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8250 (ptt-90) REVERT: B 334 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8185 (ttm170) REVERT: B 338 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8362 (mt-10) REVERT: B 391 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7604 (mmt180) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.2368 time to fit residues: 40.8984 Evaluate side-chains 138 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 218 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 272 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 46 SER 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 188 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 Chi-restraints excluded: chain B residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 249 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: 0.6885 moved from start: 0.3129 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= 0.217 Angle : 0.628 10.795 8455 Z= 0.297 Chirality : 0.042 0.388 945 Planarity : 0.003 0.023 1064 Dihedral : 9.475 85.873 973 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.16 % Allowed : 23.46 % Favored : 71.38 % 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: 1.17 (0.31), residues: 753 helix: 1.61 (0.23), residues: 522 sheet: 1.65 (0.56), residues: 63 loop : -2.33 (0.43), residues: 168 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 0.012 0.001 PHE B 207 TYR 0.008 0.001 TYR A 372 ARG 0.004 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 143 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7794 (p) cc_final: 0.7425 (p) REVERT: A 85 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5176 (tp) REVERT: A 91 MET cc_start: 0.5001 (mmp) cc_final: 0.4774 (mmp) REVERT: A 185 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: A 186 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 235 LEU cc_start: 0.8867 (tt) cc_final: 0.8418 (tt) REVERT: A 313 GLU cc_start: 0.6505 (pp20) cc_final: 0.6053 (pp20) REVERT: A 331 GLU cc_start: 0.9220 (mm-30) cc_final: 0.9012 (mm-30) REVERT: A 334 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8294 (ttm170) REVERT: A 338 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 391 ARG cc_start: 0.8226 (mmt-90) cc_final: 0.7968 (mmt-90) REVERT: B 218 GLU cc_start: 0.7406 (tt0) cc_final: 0.7169 (tt0) REVERT: B 278 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.7244 (m-70) REVERT: B 290 GLN cc_start: 0.8075 (mp10) cc_final: 0.7590 (mp10) REVERT: B 305 ILE cc_start: 0.4744 (OUTLIER) cc_final: 0.4515 (pt) REVERT: B 322 GLU cc_start: 0.8430 (pm20) cc_final: 0.7674 (pp20) REVERT: B 332 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8224 (ptt-90) REVERT: B 338 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8424 (mt-10) REVERT: B 377 ARG cc_start: 0.8266 (pmt-80) cc_final: 0.8037 (pmt-80) REVERT: B 391 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.7709 (mmt180) outliers start: 31 outliers final: 22 residues processed: 136 average time/residue: 0.2357 time to fit residues: 39.7609 Evaluate side-chains 137 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 46 SER 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 188 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 Chi-restraints excluded: chain B residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN B 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3291 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= 0.212 Angle : 0.627 10.127 8455 Z= 0.297 Chirality : 0.043 0.389 945 Planarity : 0.003 0.028 1064 Dihedral : 9.434 87.050 973 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.32 % Allowed : 23.79 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 753 helix: 1.63 (0.23), residues: 523 sheet: 1.61 (0.57), residues: 63 loop : -2.29 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.001 0.000 HIS B 136 PHE 0.012 0.001 PHE B 207 TYR 0.010 0.001 TYR A 372 ARG 0.007 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 143 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7771 (p) cc_final: 0.7411 (p) REVERT: A 85 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5110 (tp) REVERT: A 91 MET cc_start: 0.4992 (mmp) cc_final: 0.4779 (mmp) REVERT: A 185 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: A 186 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 235 LEU cc_start: 0.8884 (tt) cc_final: 0.8502 (tt) REVERT: A 289 ARG cc_start: 0.8167 (ptp-170) cc_final: 0.7775 (ptp-170) REVERT: A 313 GLU cc_start: 0.6460 (pp20) cc_final: 0.6189 (pp20) REVERT: A 331 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8992 (mm-30) REVERT: A 334 ARG cc_start: 0.8927 (ttp80) cc_final: 0.8278 (ttm170) REVERT: A 338 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 377 ARG cc_start: 0.8478 (tpm-80) cc_final: 0.8105 (tpm-80) REVERT: A 391 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.7996 (mmt-90) REVERT: B 85 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5350 (tp) REVERT: B 218 GLU cc_start: 0.7391 (tt0) cc_final: 0.7154 (tt0) REVERT: B 278 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7292 (m-70) REVERT: B 290 GLN cc_start: 0.8108 (mp10) cc_final: 0.7614 (mp10) REVERT: B 305 ILE cc_start: 0.4754 (OUTLIER) cc_final: 0.4525 (pt) REVERT: B 322 GLU cc_start: 0.8474 (pm20) cc_final: 0.8125 (pp20) REVERT: B 332 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8191 (ptt-90) REVERT: B 343 GLU cc_start: 0.7667 (pm20) cc_final: 0.7438 (pm20) REVERT: B 377 ARG cc_start: 0.8318 (pmt-80) cc_final: 0.8040 (pmt-80) REVERT: B 391 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.7696 (mmt180) outliers start: 32 outliers final: 24 residues processed: 136 average time/residue: 0.2526 time to fit residues: 42.2454 Evaluate side-chains 140 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 46 SER 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 188 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3395 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= 0.208 Angle : 0.638 9.952 8455 Z= 0.302 Chirality : 0.042 0.382 945 Planarity : 0.003 0.030 1064 Dihedral : 9.367 87.665 973 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.32 % Allowed : 24.63 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.31), residues: 753 helix: 1.61 (0.23), residues: 522 sheet: 1.56 (0.58), residues: 64 loop : -2.29 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.001 0.000 HIS A 136 PHE 0.011 0.001 PHE B 207 TYR 0.009 0.001 TYR A 372 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 146 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7761 (p) cc_final: 0.7400 (p) REVERT: A 85 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.5190 (tp) REVERT: A 91 MET cc_start: 0.4955 (mmp) cc_final: 0.4727 (mmp) REVERT: A 185 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6674 (tm-30) REVERT: A 186 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 235 LEU cc_start: 0.8887 (tt) cc_final: 0.8501 (tt) REVERT: A 272 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 313 GLU cc_start: 0.6659 (pp20) cc_final: 0.6147 (pp20) REVERT: A 331 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8976 (mm-30) REVERT: A 334 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8637 (ttm170) REVERT: A 377 ARG cc_start: 0.8464 (tpm-80) cc_final: 0.8071 (tpm-80) REVERT: A 391 ARG cc_start: 0.8256 (mmt-90) cc_final: 0.8001 (mmt-90) REVERT: B 85 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5144 (tt) REVERT: B 278 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7317 (m-70) REVERT: B 290 GLN cc_start: 0.8102 (mp10) cc_final: 0.7597 (mp10) REVERT: B 305 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4534 (pt) REVERT: B 332 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8155 (ptt-90) REVERT: B 343 GLU cc_start: 0.7701 (pm20) cc_final: 0.7482 (pm20) REVERT: B 377 ARG cc_start: 0.8316 (pmt-80) cc_final: 0.8020 (pmt-80) REVERT: B 391 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7671 (mmt180) outliers start: 32 outliers final: 24 residues processed: 139 average time/residue: 0.2409 time to fit residues: 41.3884 Evaluate side-chains 142 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain B residue 46 SER 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 188 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 368 LEU 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: 0.8980 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3509 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= 0.230 Angle : 0.649 9.850 8455 Z= 0.308 Chirality : 0.043 0.389 945 Planarity : 0.003 0.030 1064 Dihedral : 9.460 88.129 973 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.32 % Allowed : 24.79 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.31), residues: 753 helix: 1.56 (0.23), residues: 521 sheet: 1.45 (0.57), residues: 64 loop : -2.32 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.000 HIS A 136 PHE 0.012 0.002 PHE B 207 TYR 0.009 0.001 TYR A 372 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 141 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.8075 (t0) cc_final: 0.7537 (t0) REVERT: A 46 SER cc_start: 0.7785 (p) cc_final: 0.7413 (p) REVERT: A 85 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5154 (tp) REVERT: A 185 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: A 186 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 235 LEU cc_start: 0.8893 (tt) cc_final: 0.8505 (tt) REVERT: A 264 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7003 (mm) REVERT: A 289 ARG cc_start: 0.8128 (ptp-170) cc_final: 0.7762 (ptp-170) REVERT: A 313 GLU cc_start: 0.6628 (pp20) cc_final: 0.6133 (pp20) REVERT: A 331 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8896 (mm-30) REVERT: A 334 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8032 (ttm170) REVERT: A 338 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 366 MET cc_start: 0.7949 (tmm) cc_final: 0.7714 (tmm) REVERT: A 377 ARG cc_start: 0.8461 (tpm-80) cc_final: 0.8073 (tpm-80) REVERT: A 391 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7969 (mmt-90) REVERT: B 85 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5370 (tp) REVERT: B 278 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7342 (m-70) REVERT: B 290 GLN cc_start: 0.8123 (mp10) cc_final: 0.7626 (mp10) REVERT: B 305 ILE cc_start: 0.4756 (OUTLIER) cc_final: 0.4529 (pt) REVERT: B 313 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5791 (pp20) REVERT: B 332 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (ptt-90) REVERT: B 338 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 343 GLU cc_start: 0.7728 (pm20) cc_final: 0.7522 (pm20) REVERT: B 377 ARG cc_start: 0.8339 (pmt-80) cc_final: 0.8050 (pmt-80) REVERT: B 391 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7695 (mmt180) outliers start: 32 outliers final: 23 residues processed: 134 average time/residue: 0.2605 time to fit residues: 43.0578 Evaluate side-chains 139 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 264 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 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 181 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.168373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.145292 restraints weight = 10253.317| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.69 r_work: 0.3835 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6212 Z= 0.173 Angle : 0.629 9.896 8455 Z= 0.294 Chirality : 0.042 0.371 945 Planarity : 0.003 0.030 1064 Dihedral : 9.209 89.846 973 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.16 % Allowed : 25.29 % 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: 1.19 (0.32), residues: 753 helix: 1.63 (0.24), residues: 523 sheet: 1.40 (0.57), residues: 64 loop : -2.27 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.001 0.000 HIS B 344 PHE 0.009 0.001 PHE B 207 TYR 0.008 0.001 TYR A 372 ARG 0.007 0.000 ARG B 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.46 seconds wall clock time: 34 minutes 37.15 seconds (2077.15 seconds total)