Starting phenix.real_space_refine on Tue Feb 13 12:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/02_2024/7p5j_13200.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/02_2024/7p5j_13200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/02_2024/7p5j_13200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/02_2024/7p5j_13200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/02_2024/7p5j_13200.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5j_13200/02_2024/7p5j_13200.pdb" } resolution = 4.0 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4034 2.51 5 N 1036 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6250 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3069 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.81, per 1000 atoms: 0.61 Number of scatterers: 6250 At special positions: 0 Unit cell: (88.536, 71.61, 134.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1156 8.00 N 1036 7.00 C 4034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 370 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 501 " - " ASN A 284 " " NAG A 502 " - " ASN A 355 " " NAG B 501 " - " ASN B 284 " " NAG B 502 " - " ASN B 355 " " NAG C 1 " - " ASN A 130 " " NAG D 1 " - " ASN B 130 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.6 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.604A pdb=" N HIS A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 70 removed outlier: 3.591A pdb=" N GLN A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 161 Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 238 removed outlier: 3.636A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 276 removed outlier: 4.116A pdb=" N VAL A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.755A pdb=" N LEU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 335 removed outlier: 3.759A pdb=" N ARG A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.805A pdb=" N GLN A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 368 removed outlier: 3.565A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 4.183A pdb=" N SER A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.266A pdb=" N LEU A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 418 Proline residue: A 414 - end of helix removed outlier: 4.580A pdb=" N ALA A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 37 through 70 removed outlier: 3.620A pdb=" N ALA B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 161 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.694A pdb=" N ALA B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 238 removed outlier: 3.757A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 275 removed outlier: 4.010A pdb=" N VAL B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 311 through 335 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.925A pdb=" N GLN B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 368 Processing helix chain 'B' and resid 369 through 385 removed outlier: 4.120A pdb=" N LEU B 373 " --> pdb=" O HIS B 369 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 418 Proline residue: B 414 - end of helix removed outlier: 4.576A pdb=" N ALA B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1656 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: 1.64 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1975 1.34 - 1.46: 1103 1.46 - 1.58: 3270 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 6378 Sorted by residual: bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 1.517 1.545 -0.028 9.30e-03 1.16e+04 9.10e+00 bond pdb=" N VAL B 243 " pdb=" CA VAL B 243 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 8.03e+00 bond pdb=" N ASP B 137 " pdb=" CA ASP B 137 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 bond pdb=" N LEU B 242 " pdb=" CA LEU B 242 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.65e+00 ... (remaining 6373 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.19: 165 106.19 - 113.20: 3599 113.20 - 120.22: 2339 120.22 - 127.23: 2526 127.23 - 134.25: 75 Bond angle restraints: 8704 Sorted by residual: angle pdb=" N PRO A 421 " pdb=" CA PRO A 421 " pdb=" C PRO A 421 " ideal model delta sigma weight residual 110.70 116.89 -6.19 1.22e+00 6.72e-01 2.57e+01 angle pdb=" CA PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 117.93 123.81 -5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" CA PRO A 421 " pdb=" C PRO A 421 " pdb=" N PRO A 422 " ideal model delta sigma weight residual 117.93 123.57 -5.64 1.20e+00 6.94e-01 2.21e+01 angle pdb=" O PRO B 421 " pdb=" C PRO B 421 " pdb=" N PRO B 422 " ideal model delta sigma weight residual 121.46 116.44 5.02 1.18e+00 7.18e-01 1.81e+01 angle pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " pdb=" CG ASP B 137 " ideal model delta sigma weight residual 112.60 116.68 -4.08 1.00e+00 1.00e+00 1.67e+01 ... (remaining 8699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 3516 21.06 - 42.12: 296 42.12 - 63.18: 58 63.18 - 84.24: 15 84.24 - 105.30: 15 Dihedral angle restraints: 3900 sinusoidal: 1590 harmonic: 2310 Sorted by residual: dihedral pdb=" CB CYS B 303 " pdb=" SG CYS B 303 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual 93.00 9.23 83.77 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA ASP B 279 " pdb=" C ASP B 279 " pdb=" N PRO B 280 " pdb=" CA PRO B 280 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" O4 NAG C 2 " ideal model delta sinusoidal sigma weight residual 175.11 69.81 105.30 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 3897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 930 0.061 - 0.122: 131 0.122 - 0.182: 8 0.182 - 0.243: 2 0.243 - 0.304: 1 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1069 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.295 2.00e-02 2.50e+03 2.56e-01 8.19e+02 pdb=" C7 NAG D 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.454 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.266 2.00e-02 2.50e+03 2.21e-01 6.13e+02 pdb=" C7 NAG D 1 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.368 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 130 " -0.025 2.00e-02 2.50e+03 2.36e-02 6.95e+00 pdb=" CG ASN A 130 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 130 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 130 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.022 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1361 2.79 - 3.32: 6914 3.32 - 3.85: 10669 3.85 - 4.37: 11531 4.37 - 4.90: 19376 Nonbonded interactions: 49851 Sorted by model distance: nonbonded pdb=" O GLU B 154 " pdb=" OG1 THR B 157 " model vdw 2.264 2.440 nonbonded pdb=" O GLU A 154 " pdb=" OG1 THR A 157 " model vdw 2.274 2.440 nonbonded pdb=" O VAL A 90 " pdb=" OG SER A 93 " model vdw 2.286 2.440 nonbonded pdb=" O3 NAG C 1 " pdb=" O7 NAG C 2 " model vdw 2.330 2.440 nonbonded pdb=" OD1 ASN A 205 " pdb=" N VAL A 206 " model vdw 2.344 2.520 ... (remaining 49846 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.610 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: 2.650 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.760 Find NCS groups from input model: 0.310 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 0.051 6378 Z= 0.262 Angle : 0.725 7.505 8704 Z= 0.405 Chirality : 0.043 0.304 1072 Planarity : 0.011 0.256 1086 Dihedral : 17.475 105.301 2392 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.60 % Allowed : 1.51 % Favored : 97.89 % 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: 2.65 (0.31), residues: 790 helix: 2.36 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 258 HIS 0.004 0.001 HIS B 128 PHE 0.029 0.002 PHE B 208 TYR 0.026 0.002 TYR A 299 ARG 0.004 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 273 ASP cc_start: 0.7622 (t70) cc_final: 0.6956 (t70) REVERT: A 350 LEU cc_start: 0.8933 (mt) cc_final: 0.8660 (mt) REVERT: B 40 TYR cc_start: 0.7595 (t80) cc_final: 0.7385 (t80) REVERT: B 98 LEU cc_start: 0.8265 (mm) cc_final: 0.8063 (mm) REVERT: B 134 SER cc_start: 0.8916 (m) cc_final: 0.8442 (t) REVERT: B 160 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 167 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7288 (tp30) REVERT: B 304 ASN cc_start: 0.8119 (m-40) cc_final: 0.7634 (m-40) outliers start: 4 outliers final: 2 residues processed: 241 average time/residue: 0.1431 time to fit residues: 47.1068 Evaluate side-chains 204 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 244 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6378 Z= 0.216 Angle : 0.698 9.951 8704 Z= 0.322 Chirality : 0.043 0.249 1072 Planarity : 0.005 0.072 1086 Dihedral : 10.730 74.727 1024 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.27 % Allowed : 15.26 % Favored : 82.48 % 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: 3.08 (0.31), residues: 790 helix: 2.63 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.49 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 258 HIS 0.006 0.001 HIS B 138 PHE 0.033 0.002 PHE A 208 TYR 0.020 0.002 TYR A 377 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 0.718 Fit side-chains REVERT: A 40 TYR cc_start: 0.7952 (t80) cc_final: 0.7619 (t80) REVERT: A 95 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 273 ASP cc_start: 0.7604 (t70) cc_final: 0.7150 (t70) REVERT: B 134 SER cc_start: 0.8989 (m) cc_final: 0.8396 (t) REVERT: B 304 ASN cc_start: 0.8244 (m-40) cc_final: 0.7698 (m-40) REVERT: B 381 LEU cc_start: 0.8318 (mt) cc_final: 0.8075 (mp) outliers start: 15 outliers final: 12 residues processed: 215 average time/residue: 0.1440 time to fit residues: 42.6092 Evaluate side-chains 214 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 HIS B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6378 Z= 0.222 Angle : 0.678 10.289 8704 Z= 0.309 Chirality : 0.041 0.186 1072 Planarity : 0.005 0.062 1086 Dihedral : 8.005 57.183 1018 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.02 % Allowed : 17.82 % Favored : 79.15 % 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: 3.27 (0.31), residues: 790 helix: 2.78 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.48 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 258 HIS 0.006 0.001 HIS B 326 PHE 0.035 0.002 PHE B 208 TYR 0.023 0.002 TYR A 299 ARG 0.002 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 0.728 Fit side-chains REVERT: A 40 TYR cc_start: 0.8015 (t80) cc_final: 0.7675 (t80) REVERT: A 273 ASP cc_start: 0.7666 (t70) cc_final: 0.7199 (t70) REVERT: A 396 LEU cc_start: 0.9223 (mm) cc_final: 0.9010 (mm) REVERT: B 39 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 95 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8198 (mp) REVERT: B 134 SER cc_start: 0.9061 (m) cc_final: 0.8260 (t) REVERT: B 193 GLN cc_start: 0.7781 (tt0) cc_final: 0.7506 (pm20) REVERT: B 214 TRP cc_start: 0.6753 (t60) cc_final: 0.6397 (t60) REVERT: B 304 ASN cc_start: 0.8194 (m-40) cc_final: 0.7728 (m-40) REVERT: B 381 LEU cc_start: 0.8444 (mt) cc_final: 0.8053 (mt) outliers start: 20 outliers final: 15 residues processed: 213 average time/residue: 0.1472 time to fit residues: 42.7538 Evaluate side-chains 215 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 370 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7747 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6378 Z= 0.199 Angle : 0.678 10.750 8704 Z= 0.308 Chirality : 0.039 0.175 1072 Planarity : 0.005 0.058 1086 Dihedral : 6.849 56.008 1018 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.63 % Allowed : 19.94 % Favored : 76.44 % 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: 3.32 (0.30), residues: 790 helix: 2.82 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.63 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.028 0.001 PHE B 208 TYR 0.024 0.002 TYR A 299 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 0.691 Fit side-chains REVERT: A 40 TYR cc_start: 0.8036 (t80) cc_final: 0.7732 (t80) REVERT: A 273 ASP cc_start: 0.7657 (t70) cc_final: 0.7191 (t70) REVERT: A 396 LEU cc_start: 0.9196 (mm) cc_final: 0.8948 (mm) REVERT: B 39 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 134 SER cc_start: 0.9049 (m) cc_final: 0.8289 (t) REVERT: B 193 GLN cc_start: 0.7871 (tt0) cc_final: 0.7511 (pm20) REVERT: B 304 ASN cc_start: 0.8147 (m-40) cc_final: 0.7758 (m-40) REVERT: B 381 LEU cc_start: 0.8497 (mt) cc_final: 0.8116 (mt) outliers start: 24 outliers final: 19 residues processed: 220 average time/residue: 0.1416 time to fit residues: 42.8695 Evaluate side-chains 218 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 370 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.0000 overall best weight: 1.1926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6378 Z= 0.245 Angle : 0.728 12.361 8704 Z= 0.330 Chirality : 0.041 0.161 1072 Planarity : 0.005 0.053 1086 Dihedral : 6.553 55.554 1018 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.53 % Allowed : 21.75 % Favored : 73.72 % 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: 3.20 (0.30), residues: 790 helix: 2.76 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.64 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 258 HIS 0.010 0.001 HIS B 138 PHE 0.019 0.002 PHE B 208 TYR 0.026 0.002 TYR A 299 ARG 0.005 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 0.735 Fit side-chains REVERT: A 40 TYR cc_start: 0.8133 (t80) cc_final: 0.7761 (t80) REVERT: A 61 PHE cc_start: 0.7592 (m-80) cc_final: 0.7314 (m-80) REVERT: A 273 ASP cc_start: 0.7695 (t70) cc_final: 0.7162 (t70) REVERT: A 396 LEU cc_start: 0.9236 (mm) cc_final: 0.8980 (mm) REVERT: B 39 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 134 SER cc_start: 0.9112 (m) cc_final: 0.8228 (t) REVERT: B 193 GLN cc_start: 0.7872 (tt0) cc_final: 0.7416 (pm20) REVERT: B 304 ASN cc_start: 0.8141 (m-40) cc_final: 0.7682 (m-40) REVERT: B 381 LEU cc_start: 0.8425 (mt) cc_final: 0.7909 (mt) outliers start: 30 outliers final: 28 residues processed: 213 average time/residue: 0.1392 time to fit residues: 40.8736 Evaluate side-chains 227 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6378 Z= 0.219 Angle : 0.723 13.045 8704 Z= 0.329 Chirality : 0.040 0.208 1072 Planarity : 0.004 0.050 1086 Dihedral : 6.405 55.099 1018 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.68 % Allowed : 23.41 % Favored : 71.90 % 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: 3.21 (0.30), residues: 790 helix: 2.74 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 258 HIS 0.012 0.001 HIS B 138 PHE 0.018 0.002 PHE B 208 TYR 0.029 0.002 TYR A 299 ARG 0.004 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 0.747 Fit side-chains REVERT: A 40 TYR cc_start: 0.8153 (t80) cc_final: 0.7816 (t80) REVERT: A 61 PHE cc_start: 0.7517 (m-80) cc_final: 0.7233 (m-80) REVERT: A 273 ASP cc_start: 0.7697 (t70) cc_final: 0.7204 (t70) REVERT: A 330 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 333 GLU cc_start: 0.8447 (tp30) cc_final: 0.8241 (tp30) REVERT: A 396 LEU cc_start: 0.9230 (mm) cc_final: 0.8962 (mm) REVERT: B 39 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 134 SER cc_start: 0.8889 (m) cc_final: 0.7995 (t) REVERT: B 193 GLN cc_start: 0.7841 (tt0) cc_final: 0.7434 (pm20) REVERT: B 304 ASN cc_start: 0.8131 (m-40) cc_final: 0.7860 (t0) REVERT: B 381 LEU cc_start: 0.8434 (mt) cc_final: 0.7919 (mt) outliers start: 31 outliers final: 27 residues processed: 219 average time/residue: 0.1379 time to fit residues: 41.8676 Evaluate side-chains 224 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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: 0.7754 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6378 Z= 0.206 Angle : 0.724 13.700 8704 Z= 0.326 Chirality : 0.040 0.226 1072 Planarity : 0.004 0.048 1086 Dihedral : 6.249 54.961 1018 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.23 % Allowed : 24.02 % Favored : 71.75 % 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: 3.22 (0.30), residues: 790 helix: 2.75 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.51 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 258 HIS 0.016 0.001 HIS B 138 PHE 0.018 0.002 PHE B 208 TYR 0.026 0.002 TYR A 299 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8166 (t80) cc_final: 0.7827 (t80) REVERT: A 61 PHE cc_start: 0.7503 (m-80) cc_final: 0.7220 (m-80) REVERT: A 273 ASP cc_start: 0.7674 (t70) cc_final: 0.7226 (t70) REVERT: A 330 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8573 (mt) REVERT: A 353 THR cc_start: 0.8865 (t) cc_final: 0.8618 (t) REVERT: A 396 LEU cc_start: 0.9221 (mm) cc_final: 0.8952 (mm) REVERT: B 39 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 134 SER cc_start: 0.8824 (m) cc_final: 0.7895 (t) REVERT: B 193 GLN cc_start: 0.7835 (tt0) cc_final: 0.7443 (pm20) REVERT: B 304 ASN cc_start: 0.8084 (m-40) cc_final: 0.7842 (t0) REVERT: B 381 LEU cc_start: 0.8432 (mt) cc_final: 0.7848 (mt) outliers start: 28 outliers final: 24 residues processed: 216 average time/residue: 0.1357 time to fit residues: 40.7237 Evaluate side-chains 224 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.0060 chunk 42 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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: 0.7745 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6378 Z= 0.207 Angle : 0.739 13.705 8704 Z= 0.331 Chirality : 0.041 0.226 1072 Planarity : 0.004 0.047 1086 Dihedral : 6.076 54.747 1018 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.53 % Allowed : 24.77 % Favored : 70.69 % 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: 3.26 (0.30), residues: 790 helix: 2.76 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.44 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.017 0.001 PHE B 208 TYR 0.021 0.002 TYR A 299 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 0.704 Fit side-chains REVERT: A 40 TYR cc_start: 0.8163 (t80) cc_final: 0.7841 (t80) REVERT: A 61 PHE cc_start: 0.7251 (m-80) cc_final: 0.6989 (m-80) REVERT: A 273 ASP cc_start: 0.7613 (t70) cc_final: 0.7104 (t70) REVERT: A 330 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 396 LEU cc_start: 0.9222 (mm) cc_final: 0.8941 (mm) REVERT: B 39 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 134 SER cc_start: 0.8965 (m) cc_final: 0.8184 (t) REVERT: B 193 GLN cc_start: 0.7913 (tt0) cc_final: 0.7436 (pm20) REVERT: B 304 ASN cc_start: 0.8059 (m-40) cc_final: 0.7857 (t0) REVERT: B 309 ASN cc_start: 0.8767 (m-40) cc_final: 0.8456 (m-40) REVERT: B 381 LEU cc_start: 0.8424 (mt) cc_final: 0.7824 (mt) outliers start: 30 outliers final: 26 residues processed: 217 average time/residue: 0.1387 time to fit residues: 41.5167 Evaluate side-chains 220 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 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 360 ASN B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6378 Z= 0.225 Angle : 0.760 14.174 8704 Z= 0.342 Chirality : 0.041 0.243 1072 Planarity : 0.004 0.048 1086 Dihedral : 6.008 54.484 1018 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.08 % Allowed : 25.98 % Favored : 69.94 % 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: 3.25 (0.30), residues: 790 helix: 2.74 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.31 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.017 0.001 PHE B 208 TYR 0.021 0.002 TYR A 299 ARG 0.007 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 0.725 Fit side-chains REVERT: A 40 TYR cc_start: 0.8160 (t80) cc_final: 0.7820 (t80) REVERT: A 61 PHE cc_start: 0.7251 (m-80) cc_final: 0.6992 (m-80) REVERT: A 139 LEU cc_start: 0.9364 (tp) cc_final: 0.9079 (tt) REVERT: A 273 ASP cc_start: 0.7647 (t70) cc_final: 0.7069 (t70) REVERT: A 330 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 396 LEU cc_start: 0.9231 (mm) cc_final: 0.8941 (mm) REVERT: B 39 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 134 SER cc_start: 0.9092 (m) cc_final: 0.8264 (t) REVERT: B 193 GLN cc_start: 0.7953 (tt0) cc_final: 0.7485 (pm20) REVERT: B 381 LEU cc_start: 0.8435 (mt) cc_final: 0.7837 (mt) outliers start: 27 outliers final: 25 residues processed: 209 average time/residue: 0.1352 time to fit residues: 39.2552 Evaluate side-chains 221 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6378 Z= 0.237 Angle : 0.765 13.943 8704 Z= 0.348 Chirality : 0.041 0.276 1072 Planarity : 0.005 0.050 1086 Dihedral : 6.006 53.748 1018 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.08 % Allowed : 25.83 % Favored : 70.09 % 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: 3.23 (0.30), residues: 790 helix: 2.73 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.32 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 258 HIS 0.006 0.001 HIS B 326 PHE 0.018 0.001 PHE B 208 TYR 0.015 0.002 TYR A 299 ARG 0.003 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 0.654 Fit side-chains REVERT: A 40 TYR cc_start: 0.8187 (t80) cc_final: 0.7823 (t80) REVERT: A 61 PHE cc_start: 0.7255 (m-80) cc_final: 0.6997 (m-80) REVERT: A 273 ASP cc_start: 0.7615 (t70) cc_final: 0.7042 (t70) REVERT: A 330 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8614 (mt) REVERT: A 396 LEU cc_start: 0.9246 (mm) cc_final: 0.8950 (mm) REVERT: B 39 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 134 SER cc_start: 0.9114 (m) cc_final: 0.8269 (t) REVERT: B 193 GLN cc_start: 0.7881 (tt0) cc_final: 0.7451 (pm20) REVERT: B 246 MET cc_start: 0.7718 (ppp) cc_final: 0.6230 (ppp) REVERT: B 330 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 381 LEU cc_start: 0.8458 (mt) cc_final: 0.7881 (mt) outliers start: 27 outliers final: 23 residues processed: 212 average time/residue: 0.1341 time to fit residues: 39.5835 Evaluate side-chains 219 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 41 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135632 restraints weight = 9901.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139096 restraints weight = 5912.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141455 restraints weight = 4046.609| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6378 Z= 0.209 Angle : 0.749 14.381 8704 Z= 0.339 Chirality : 0.040 0.268 1072 Planarity : 0.004 0.056 1086 Dihedral : 5.851 53.410 1018 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.47 % Allowed : 26.74 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.29 (0.30), residues: 790 helix: 2.77 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.46 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 258 HIS 0.005 0.001 HIS B 326 PHE 0.016 0.001 PHE B 208 TYR 0.013 0.001 TYR A 377 ARG 0.003 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.15 seconds wall clock time: 27 minutes 59.95 seconds (1679.95 seconds total)