Starting phenix.real_space_refine on Mon Sep 23 23:25:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/09_2024/7vq4_32085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/09_2024/7vq4_32085.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/7vq4_32085/09_2024/7vq4_32085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/09_2024/7vq4_32085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/09_2024/7vq4_32085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/09_2024/7vq4_32085.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6306 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Time building chain proxies: 4.19, per 1000 atoms: 0.66 Number of scatterers: 6306 At special positions: 0 Unit cell: (82.134, 84.162, 111.54, 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 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 950.3 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.624A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.863A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.756A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.524A pdb=" N LYS A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 Processing helix chain 'A' and resid 187 through 214 removed outlier: 3.694A pdb=" N ASP A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.738A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.624A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.864A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.757A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.523A pdb=" N LYS B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 Processing helix chain 'B' and resid 187 through 214 removed outlier: 3.693A pdb=" N ASP B 191 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.737A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 509 hydrogen bonds defined for protein. 1527 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: 1.90 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: 2008 1.34 - 1.46: 1045 1.46 - 1.57: 3321 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB TRP B 57 " pdb=" CG TRP B 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP A 57 " pdb=" CG TRP A 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP B 187 " pdb=" CG TRP B 187 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.63e+00 bond pdb=" CB TRP A 187 " pdb=" CG TRP A 187 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.62e+00 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.14e+00 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 8313 1.50 - 3.01: 299 3.01 - 4.51: 56 4.51 - 6.01: 20 6.01 - 7.52: 4 Bond angle restraints: 8692 Sorted by residual: angle pdb=" N VAL B 105 " pdb=" CA VAL B 105 " pdb=" C VAL B 105 " ideal model delta sigma weight residual 112.17 108.66 3.51 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N VAL A 105 " pdb=" CA VAL A 105 " pdb=" C VAL A 105 " ideal model delta sigma weight residual 112.17 108.67 3.50 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N PHE B 134 " pdb=" CA PHE B 134 " pdb=" C PHE B 134 " ideal model delta sigma weight residual 110.44 114.21 -3.77 1.20e+00 6.94e-01 9.89e+00 angle pdb=" N PHE A 134 " pdb=" CA PHE A 134 " pdb=" C PHE A 134 " ideal model delta sigma weight residual 110.44 114.16 -3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" CA PRO B 267 " pdb=" C PRO B 267 " pdb=" O PRO B 267 " ideal model delta sigma weight residual 123.07 119.36 3.71 1.38e+00 5.25e-01 7.22e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 3396 18.03 - 36.05: 366 36.05 - 54.08: 62 54.08 - 72.10: 26 72.10 - 90.13: 6 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS A 184 " pdb=" C CYS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA CYS B 184 " pdb=" C CYS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 499 0.030 - 0.060: 357 0.060 - 0.090: 105 0.090 - 0.119: 30 0.119 - 0.149: 5 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" C PRO B 365 " pdb=" CB PRO B 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO A 365 " pdb=" N PRO A 365 " pdb=" C PRO A 365 " pdb=" CB PRO A 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 365 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 365 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 127 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 128 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " 0.021 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 239 2.70 - 3.25: 6944 3.25 - 3.80: 10031 3.80 - 4.35: 11847 4.35 - 4.90: 20167 Nonbonded interactions: 49228 Sorted by model distance: nonbonded pdb=" OD1 ASP A 295 " pdb=" N PHE A 296 " model vdw 2.155 3.120 nonbonded pdb=" OD1 ASP B 295 " pdb=" N PHE B 296 " model vdw 2.155 3.120 nonbonded pdb=" O MET B 1 " pdb=" N ARG B 5 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG A 80 " pdb=" OH TYR A 136 " model vdw 2.225 3.120 ... (remaining 49223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.150 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.007 0.044 6434 Z= 0.439 Angle : 0.740 7.518 8692 Z= 0.423 Chirality : 0.042 0.149 996 Planarity : 0.004 0.050 1090 Dihedral : 16.105 90.127 2352 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.30 % Allowed : 8.62 % Favored : 89.08 % 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: -1.96 (0.27), residues: 792 helix: -0.72 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -3.76 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 266 PHE 0.018 0.002 PHE B 153 TYR 0.013 0.002 TYR B 291 ARG 0.003 0.001 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 0.718 Fit side-chains REVERT: A 40 TYR cc_start: 0.8043 (t80) cc_final: 0.7503 (t80) REVERT: A 180 SER cc_start: 0.9003 (t) cc_final: 0.8580 (p) REVERT: A 237 LYS cc_start: 0.8450 (mttt) cc_final: 0.8150 (mtmt) REVERT: A 306 LEU cc_start: 0.8688 (tp) cc_final: 0.8481 (tp) REVERT: A 307 GLU cc_start: 0.7515 (pt0) cc_final: 0.7258 (pm20) REVERT: A 322 LYS cc_start: 0.7820 (tptm) cc_final: 0.7412 (ttpt) REVERT: B 1 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4477 (ptp) REVERT: B 40 TYR cc_start: 0.8064 (t80) cc_final: 0.7540 (t80) REVERT: B 328 LEU cc_start: 0.9183 (tp) cc_final: 0.8902 (tp) outliers start: 16 outliers final: 7 residues processed: 216 average time/residue: 0.2269 time to fit residues: 60.8971 Evaluate side-chains 162 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 223 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 54 ASN A 251 ASN A 259 HIS A 293 ASN A 297 GLN A 340 HIS A 343 ASN B 24 HIS B 54 ASN B 251 ASN B 259 HIS B 280 GLN B 293 ASN B 297 GLN B 330 GLN B 340 HIS B 343 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6434 Z= 0.199 Angle : 0.562 5.791 8692 Z= 0.296 Chirality : 0.038 0.142 996 Planarity : 0.004 0.047 1090 Dihedral : 5.546 49.915 870 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.89 % Allowed : 15.66 % Favored : 79.45 % 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: 1.20 (0.30), residues: 792 helix: 1.55 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.20 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 57 HIS 0.003 0.001 HIS A 259 PHE 0.013 0.001 PHE A 145 TYR 0.014 0.001 TYR A 291 ARG 0.006 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.6399 (OUTLIER) cc_final: 0.6048 (t) REVERT: A 180 SER cc_start: 0.8845 (t) cc_final: 0.8441 (p) REVERT: A 193 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.6973 (t-90) REVERT: A 237 LYS cc_start: 0.8388 (mttt) cc_final: 0.8112 (mtmt) REVERT: A 263 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7268 (tmt170) REVERT: A 286 ASP cc_start: 0.8292 (t70) cc_final: 0.7969 (t0) REVERT: A 322 LYS cc_start: 0.7633 (tptm) cc_final: 0.7089 (ttpt) REVERT: B 1 MET cc_start: 0.4631 (ttt) cc_final: 0.4392 (tpp) REVERT: B 9 ARG cc_start: 0.6486 (mtt-85) cc_final: 0.5755 (ptp90) REVERT: B 193 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7090 (t-90) REVERT: B 237 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7958 (mtmt) REVERT: B 328 LEU cc_start: 0.9039 (tp) cc_final: 0.8653 (tp) REVERT: B 377 MET cc_start: 0.8311 (mmt) cc_final: 0.8030 (mmm) outliers start: 34 outliers final: 19 residues processed: 186 average time/residue: 0.1731 time to fit residues: 42.3506 Evaluate side-chains 170 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 266 HIS A 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6434 Z= 0.265 Angle : 0.593 6.055 8692 Z= 0.310 Chirality : 0.038 0.161 996 Planarity : 0.004 0.050 1090 Dihedral : 4.816 38.763 866 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 6.03 % Allowed : 17.67 % Favored : 76.29 % 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: 1.76 (0.30), residues: 792 helix: 1.89 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -2.95 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.005 0.001 HIS B 95 PHE 0.014 0.002 PHE B 141 TYR 0.011 0.002 TYR B 236 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6205 (t) REVERT: A 193 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7076 (t-90) REVERT: A 322 LYS cc_start: 0.7554 (tptm) cc_final: 0.6904 (ttpt) REVERT: A 377 MET cc_start: 0.8283 (mmt) cc_final: 0.7936 (mmm) REVERT: B 1 MET cc_start: 0.5346 (ttt) cc_final: 0.4881 (tpp) REVERT: B 90 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7528 (mp) REVERT: B 193 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7230 (t-90) REVERT: B 328 LEU cc_start: 0.9066 (tp) cc_final: 0.8685 (tp) REVERT: B 377 MET cc_start: 0.8296 (mmt) cc_final: 0.7959 (mmm) outliers start: 42 outliers final: 28 residues processed: 181 average time/residue: 0.1517 time to fit residues: 37.3239 Evaluate side-chains 180 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6434 Z= 0.198 Angle : 0.547 6.263 8692 Z= 0.284 Chirality : 0.037 0.154 996 Planarity : 0.004 0.049 1090 Dihedral : 4.458 28.301 866 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.75 % Allowed : 18.97 % Favored : 75.29 % 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: 2.36 (0.30), residues: 792 helix: 2.26 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -2.49 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS B 259 PHE 0.011 0.001 PHE B 141 TYR 0.015 0.001 TYR A 236 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7045 (t-90) REVERT: A 321 MET cc_start: 0.7473 (mmt) cc_final: 0.7240 (mmt) REVERT: A 322 LYS cc_start: 0.7511 (tptm) cc_final: 0.6827 (ttpt) REVERT: B 1 MET cc_start: 0.5252 (ttt) cc_final: 0.4757 (tpp) REVERT: B 106 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: B 193 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: B 284 ARG cc_start: 0.7878 (mpt90) cc_final: 0.7641 (mmt90) REVERT: B 286 ASP cc_start: 0.8366 (t70) cc_final: 0.8121 (t0) REVERT: B 328 LEU cc_start: 0.8996 (tp) cc_final: 0.8635 (tp) outliers start: 40 outliers final: 27 residues processed: 174 average time/residue: 0.1560 time to fit residues: 36.7875 Evaluate side-chains 164 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6434 Z= 0.169 Angle : 0.540 7.234 8692 Z= 0.277 Chirality : 0.037 0.219 996 Planarity : 0.004 0.050 1090 Dihedral : 4.052 22.886 864 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.17 % Allowed : 20.83 % Favored : 73.99 % 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: 2.93 (0.31), residues: 792 helix: 2.65 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -2.05 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.013 0.001 PHE B 141 TYR 0.014 0.001 TYR A 236 ARG 0.007 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.6882 (t-90) REVERT: A 193 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6631 (t-90) REVERT: A 237 LYS cc_start: 0.8246 (mttp) cc_final: 0.8031 (mmmt) REVERT: A 321 MET cc_start: 0.7410 (mmt) cc_final: 0.7155 (mmt) REVERT: A 322 LYS cc_start: 0.7511 (tptm) cc_final: 0.6826 (ttpt) REVERT: A 377 MET cc_start: 0.8153 (mmt) cc_final: 0.7903 (mmm) REVERT: A 405 MET cc_start: 0.3143 (mpp) cc_final: 0.2542 (mmp) REVERT: B 1 MET cc_start: 0.5375 (ttt) cc_final: 0.4862 (tpp) REVERT: B 193 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6775 (t-90) REVERT: B 286 ASP cc_start: 0.8373 (t70) cc_final: 0.8169 (t0) REVERT: B 328 LEU cc_start: 0.8875 (tp) cc_final: 0.8510 (tp) REVERT: B 331 MET cc_start: 0.8235 (mmm) cc_final: 0.8031 (mmm) outliers start: 36 outliers final: 28 residues processed: 173 average time/residue: 0.1578 time to fit residues: 37.1200 Evaluate side-chains 170 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.167 Angle : 0.556 7.946 8692 Z= 0.279 Chirality : 0.036 0.207 996 Planarity : 0.003 0.050 1090 Dihedral : 3.922 23.138 862 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.46 % Allowed : 20.98 % Favored : 73.56 % 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: 3.09 (0.31), residues: 792 helix: 2.73 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.90 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS A 259 PHE 0.014 0.001 PHE B 145 TYR 0.013 0.001 TYR A 236 ARG 0.005 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.6875 (t-90) REVERT: A 193 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6673 (t-90) REVERT: A 237 LYS cc_start: 0.8240 (mttp) cc_final: 0.8025 (mmmt) REVERT: A 321 MET cc_start: 0.7355 (mmt) cc_final: 0.7096 (mmt) REVERT: A 322 LYS cc_start: 0.7552 (tptm) cc_final: 0.6831 (ttpt) REVERT: A 328 LEU cc_start: 0.8237 (tp) cc_final: 0.7944 (tp) REVERT: A 405 MET cc_start: 0.2752 (mpp) cc_final: 0.2150 (mmp) REVERT: B 1 MET cc_start: 0.5528 (ttt) cc_final: 0.5005 (tpp) REVERT: B 193 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6708 (t-90) REVERT: B 286 ASP cc_start: 0.8382 (t70) cc_final: 0.8177 (t0) REVERT: B 331 MET cc_start: 0.8287 (mmm) cc_final: 0.7934 (mmm) outliers start: 38 outliers final: 29 residues processed: 171 average time/residue: 0.1599 time to fit residues: 37.1803 Evaluate side-chains 171 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6434 Z= 0.175 Angle : 0.597 13.204 8692 Z= 0.291 Chirality : 0.037 0.202 996 Planarity : 0.004 0.050 1090 Dihedral : 3.940 23.341 862 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.89 % Allowed : 21.41 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.07 (0.31), residues: 792 helix: 2.69 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.95 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.010 0.001 PHE B 141 TYR 0.013 0.001 TYR A 236 ARG 0.007 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8181 (tp) cc_final: 0.7977 (mt) REVERT: A 95 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.6921 (t-90) REVERT: A 193 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6749 (t-90) REVERT: A 321 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7091 (mmt) REVERT: A 322 LYS cc_start: 0.7566 (tptm) cc_final: 0.6857 (ttpt) REVERT: A 405 MET cc_start: 0.2883 (mpp) cc_final: 0.2281 (mmp) REVERT: B 1 MET cc_start: 0.5649 (ttt) cc_final: 0.5216 (tpp) REVERT: B 193 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6874 (t-90) REVERT: B 284 ARG cc_start: 0.7713 (mpt90) cc_final: 0.7417 (mpt90) REVERT: B 286 ASP cc_start: 0.8382 (t70) cc_final: 0.8174 (t0) outliers start: 41 outliers final: 33 residues processed: 170 average time/residue: 0.1622 time to fit residues: 37.4124 Evaluate side-chains 176 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- 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: 0.7588 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.176 Angle : 0.613 14.235 8692 Z= 0.298 Chirality : 0.037 0.201 996 Planarity : 0.004 0.047 1090 Dihedral : 3.942 23.775 862 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.75 % Allowed : 21.84 % Favored : 72.41 % 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: 3.12 (0.31), residues: 792 helix: 2.70 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.82 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS A 259 PHE 0.015 0.001 PHE B 145 TYR 0.013 0.001 TYR A 236 ARG 0.007 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8147 (tp) cc_final: 0.7945 (mt) REVERT: A 95 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.6904 (t-90) REVERT: A 193 HIS cc_start: 0.7413 (OUTLIER) cc_final: 0.6715 (t-90) REVERT: A 321 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7082 (mmt) REVERT: A 322 LYS cc_start: 0.7577 (tptm) cc_final: 0.6862 (ttpt) REVERT: A 405 MET cc_start: 0.2839 (mpp) cc_final: 0.2350 (mmp) REVERT: B 193 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.6848 (t-90) REVERT: B 286 ASP cc_start: 0.8375 (t70) cc_final: 0.8169 (t0) outliers start: 40 outliers final: 30 residues processed: 164 average time/residue: 0.1648 time to fit residues: 37.2027 Evaluate side-chains 173 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.0470 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- 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: 0.7603 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6434 Z= 0.187 Angle : 0.628 14.430 8692 Z= 0.305 Chirality : 0.037 0.202 996 Planarity : 0.004 0.048 1090 Dihedral : 3.957 23.859 862 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.75 % Allowed : 21.98 % Favored : 72.27 % 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: 3.11 (0.31), residues: 792 helix: 2.69 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.76 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.010 0.001 PHE B 141 TYR 0.013 0.001 TYR A 236 ARG 0.007 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.6946 (t-90) REVERT: A 193 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6715 (t-90) REVERT: A 321 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7105 (mmt) REVERT: A 322 LYS cc_start: 0.7594 (tptm) cc_final: 0.6874 (ttpt) REVERT: A 405 MET cc_start: 0.2817 (mpp) cc_final: 0.2327 (mmp) REVERT: B 193 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.6884 (t-90) REVERT: B 286 ASP cc_start: 0.8338 (t70) cc_final: 0.8129 (t0) REVERT: B 307 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: B 331 MET cc_start: 0.8334 (mmm) cc_final: 0.8103 (mmm) outliers start: 40 outliers final: 29 residues processed: 172 average time/residue: 0.1543 time to fit residues: 36.1527 Evaluate side-chains 173 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6434 Z= 0.178 Angle : 0.621 14.550 8692 Z= 0.303 Chirality : 0.037 0.201 996 Planarity : 0.003 0.045 1090 Dihedral : 3.979 24.871 862 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.89 % Allowed : 23.13 % Favored : 71.98 % 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: 3.12 (0.31), residues: 792 helix: 2.69 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.73 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.004 0.001 HIS B 259 PHE 0.018 0.001 PHE B 145 TYR 0.014 0.001 TYR A 236 ARG 0.006 0.000 ARG B 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8231 (mt) cc_final: 0.7971 (mp) REVERT: A 95 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.6908 (t-90) REVERT: A 193 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6630 (t-90) REVERT: A 321 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7065 (mmt) REVERT: A 322 LYS cc_start: 0.7585 (tptm) cc_final: 0.6865 (ttpt) REVERT: A 375 VAL cc_start: 0.9221 (t) cc_final: 0.9002 (m) REVERT: A 405 MET cc_start: 0.2781 (mpp) cc_final: 0.2294 (mmp) REVERT: B 193 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6771 (t-90) REVERT: B 286 ASP cc_start: 0.8325 (t70) cc_final: 0.8120 (t0) REVERT: B 307 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7190 (pm20) REVERT: B 322 LYS cc_start: 0.7642 (ttpt) cc_final: 0.6695 (tppt) REVERT: B 331 MET cc_start: 0.8304 (mmm) cc_final: 0.8079 (mmm) outliers start: 34 outliers final: 28 residues processed: 171 average time/residue: 0.1496 time to fit residues: 35.6532 Evaluate side-chains 171 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 307 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126255 restraints weight = 9238.837| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.58 r_work: 0.3558 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6434 Z= 0.254 Angle : 0.674 13.850 8692 Z= 0.333 Chirality : 0.039 0.203 996 Planarity : 0.004 0.047 1090 Dihedral : 4.132 23.006 862 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.60 % Allowed : 24.57 % Favored : 70.83 % 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: 2.92 (0.31), residues: 792 helix: 2.55 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.76 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 187 HIS 0.003 0.001 HIS B 95 PHE 0.014 0.001 PHE A 206 TYR 0.012 0.001 TYR A 40 ARG 0.006 0.001 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.92 seconds wall clock time: 30 minutes 47.75 seconds (1847.75 seconds total)