Starting phenix.real_space_refine on Tue Sep 24 06:37:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/09_2024/7xja_33223.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/09_2024/7xja_33223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/09_2024/7xja_33223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/09_2024/7xja_33223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/09_2024/7xja_33223.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xja_33223/09_2024/7xja_33223.cif" } resolution = 3.5 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= 0.003 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 44 5.16 5 C 4808 2.51 5 N 1184 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7276 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3638 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 22, 'TRANS': 449} Chain: "B" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3638 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 22, 'TRANS': 449} Time building chain proxies: 4.64, per 1000 atoms: 0.64 Number of scatterers: 7276 At special positions: 0 Unit cell: (80.413, 113.573, 79.584, 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 44 16.00 O 1240 8.00 N 1184 7.00 C 4808 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: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 3 sheets defined 81.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 129 through 156 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 181 through 198 Processing helix chain 'A' and resid 204 through 225 Processing helix chain 'A' and resid 226 through 231 removed outlier: 6.910A pdb=" N ILE A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.609A pdb=" N PHE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.614A pdb=" N SER A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.514A pdb=" N GLN A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.556A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.726A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 430 through 450 removed outlier: 4.142A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.872A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.425A pdb=" N VAL A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 549 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'B' and resid 90 through 126 removed outlier: 3.514A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.854A pdb=" N LEU B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 7.085A pdb=" N ILE B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.647A pdb=" N PHE B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.716A pdb=" N VAL B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.574A pdb=" N ALA B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.674A pdb=" N GLN B 385 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 430 through 450 removed outlier: 4.073A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.866A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 549 Processing helix chain 'B' and resid 551 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487 569 hydrogen bonds defined for protein. 1635 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: 2.13 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2238 1.35 - 1.46: 1850 1.46 - 1.58: 3298 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 7460 Sorted by residual: bond pdb=" CA VAL A 175 " pdb=" CB VAL A 175 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.11e-02 8.12e+03 9.56e-01 bond pdb=" N PRO B 453 " pdb=" CA PRO B 453 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.45e-01 bond pdb=" N PRO A 453 " pdb=" CA PRO A 453 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.26e-01 bond pdb=" CA VAL B 175 " pdb=" CB VAL B 175 " ideal model delta sigma weight residual 1.530 1.540 -0.011 1.11e-02 8.12e+03 8.99e-01 bond pdb=" CB PRO A 381 " pdb=" CG PRO A 381 " ideal model delta sigma weight residual 1.492 1.447 0.045 5.00e-02 4.00e+02 8.13e-01 ... (remaining 7455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 9958 1.74 - 3.49: 167 3.49 - 5.23: 24 5.23 - 6.97: 7 6.97 - 8.72: 4 Bond angle restraints: 10160 Sorted by residual: angle pdb=" CB MET B 167 " pdb=" CG MET B 167 " pdb=" SD MET B 167 " ideal model delta sigma weight residual 112.70 103.98 8.72 3.00e+00 1.11e-01 8.44e+00 angle pdb=" CB MET A 167 " pdb=" CG MET A 167 " pdb=" SD MET A 167 " ideal model delta sigma weight residual 112.70 104.08 8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" C TYR B 230 " pdb=" N GLU B 231 " pdb=" CA GLU B 231 " ideal model delta sigma weight residual 121.94 116.23 5.71 2.00e+00 2.50e-01 8.16e+00 angle pdb=" CB MET A 460 " pdb=" CG MET A 460 " pdb=" SD MET A 460 " ideal model delta sigma weight residual 112.70 120.99 -8.29 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB MET B 360 " pdb=" CG MET B 360 " pdb=" SD MET B 360 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 ... (remaining 10155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 3975 16.10 - 32.21: 260 32.21 - 48.31: 70 48.31 - 64.41: 17 64.41 - 80.52: 20 Dihedral angle restraints: 4342 sinusoidal: 1636 harmonic: 2706 Sorted by residual: dihedral pdb=" CG ARG A 558 " pdb=" CD ARG A 558 " pdb=" NE ARG A 558 " pdb=" CZ ARG A 558 " ideal model delta sinusoidal sigma weight residual -180.00 -138.50 -41.50 2 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CG ARG B 558 " pdb=" CD ARG B 558 " pdb=" NE ARG B 558 " pdb=" CZ ARG B 558 " ideal model delta sinusoidal sigma weight residual -180.00 -138.57 -41.43 2 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " pdb=" NE ARG A 350 " pdb=" CZ ARG A 350 " ideal model delta sinusoidal sigma weight residual -180.00 -138.90 -41.10 2 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 734 0.029 - 0.057: 286 0.057 - 0.086: 125 0.086 - 0.114: 44 0.114 - 0.143: 11 Chirality restraints: 1200 Sorted by residual: chirality pdb=" CA GLU B 231 " pdb=" N GLU B 231 " pdb=" C GLU B 231 " pdb=" CB GLU B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE B 284 " pdb=" N PHE B 284 " pdb=" C PHE B 284 " pdb=" CB PHE B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL B 454 " pdb=" N VAL B 454 " pdb=" C VAL B 454 " pdb=" CB VAL B 454 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1197 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " -0.019 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP A 444 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 444 " 0.012 2.00e-02 2.50e+03 1.25e-02 3.89e+00 pdb=" CG TRP B 444 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 444 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 444 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 444 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 379 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 380 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.022 5.00e-02 4.00e+02 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 271 2.73 - 3.27: 7852 3.27 - 3.81: 12578 3.81 - 4.36: 13994 4.36 - 4.90: 24526 Nonbonded interactions: 59221 Sorted by model distance: nonbonded pdb=" O GLU B 166 " pdb=" OG1 THR B 169 " model vdw 2.182 3.040 nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR A 499 " model vdw 2.222 3.040 nonbonded pdb=" OE2 GLU B 320 " pdb=" OH TYR B 499 " model vdw 2.226 3.040 nonbonded pdb=" O GLU A 166 " pdb=" OG1 THR A 169 " model vdw 2.233 3.040 nonbonded pdb=" O ASP A 402 " pdb=" NH1 ARG A 471 " model vdw 2.284 3.120 ... (remaining 59216 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 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: 0.960 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.950 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.003 0.045 7460 Z= 0.170 Angle : 0.596 8.715 10160 Z= 0.332 Chirality : 0.039 0.143 1200 Planarity : 0.004 0.040 1256 Dihedral : 13.731 80.517 2598 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 1.81 (0.28), residues: 940 helix: 1.78 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.40 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 444 HIS 0.012 0.002 HIS B 210 PHE 0.021 0.001 PHE B 147 TYR 0.016 0.001 TYR A 140 ARG 0.011 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.7116 (tt) cc_final: 0.6626 (pt) REVERT: A 170 ILE cc_start: 0.9021 (mm) cc_final: 0.8773 (mm) REVERT: A 288 ILE cc_start: 0.7953 (mm) cc_final: 0.7742 (mt) REVERT: A 309 ARG cc_start: 0.6199 (ttp-170) cc_final: 0.5062 (mmt-90) REVERT: A 374 ILE cc_start: 0.7585 (tt) cc_final: 0.7118 (mt) REVERT: A 433 LEU cc_start: 0.7917 (tp) cc_final: 0.7463 (mt) REVERT: A 515 VAL cc_start: 0.8225 (t) cc_final: 0.7969 (t) REVERT: B 153 GLN cc_start: 0.7612 (tp40) cc_final: 0.7344 (tm-30) REVERT: B 309 ARG cc_start: 0.5313 (mtm180) cc_final: 0.4758 (mmt-90) REVERT: B 320 GLU cc_start: 0.6376 (mt-10) cc_final: 0.5887 (mt-10) REVERT: B 433 LEU cc_start: 0.8048 (tp) cc_final: 0.7664 (mt) REVERT: B 477 MET cc_start: 0.7560 (ttm) cc_final: 0.7334 (ttt) REVERT: B 540 LEU cc_start: 0.8499 (mt) cc_final: 0.8255 (mp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1898 time to fit residues: 70.0287 Evaluate side-chains 179 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.0270 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 542 ASN A 546 GLN B 542 ASN B 546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7460 Z= 0.213 Angle : 0.582 8.146 10160 Z= 0.301 Chirality : 0.042 0.192 1200 Planarity : 0.005 0.040 1256 Dihedral : 3.563 14.796 1002 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.74 % Allowed : 10.18 % Favored : 87.08 % 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: 2.43 (0.28), residues: 940 helix: 2.22 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -0.19 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 444 HIS 0.005 0.002 HIS A 513 PHE 0.019 0.002 PHE A 185 TYR 0.013 0.002 TYR B 340 ARG 0.004 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.782 Fit side-chains REVERT: A 131 LEU cc_start: 0.7477 (tt) cc_final: 0.6990 (pt) REVERT: A 142 VAL cc_start: 0.8563 (t) cc_final: 0.8336 (m) REVERT: A 309 ARG cc_start: 0.6546 (ttp-170) cc_final: 0.5247 (mmt-90) REVERT: A 408 ARG cc_start: 0.4666 (mmp-170) cc_final: 0.4064 (tpp-160) REVERT: A 433 LEU cc_start: 0.7849 (tp) cc_final: 0.7586 (mt) REVERT: B 108 MET cc_start: 0.7663 (mtt) cc_final: 0.7326 (mtp) REVERT: B 142 VAL cc_start: 0.8616 (t) cc_final: 0.8357 (m) REVERT: B 222 PHE cc_start: 0.6958 (t80) cc_final: 0.5034 (m-80) REVERT: B 309 ARG cc_start: 0.5455 (mtm180) cc_final: 0.4851 (mmt-90) REVERT: B 320 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6365 (mt-10) REVERT: B 395 GLU cc_start: 0.7338 (tp30) cc_final: 0.7119 (mt-10) REVERT: B 408 ARG cc_start: 0.3810 (mmm160) cc_final: 0.3361 (tpp-160) REVERT: B 433 LEU cc_start: 0.8050 (tp) cc_final: 0.7690 (mt) REVERT: B 477 MET cc_start: 0.7697 (ttm) cc_final: 0.7489 (ttt) REVERT: B 483 ASP cc_start: 0.6720 (t70) cc_final: 0.6405 (t0) REVERT: B 540 LEU cc_start: 0.8576 (mt) cc_final: 0.8360 (mt) outliers start: 21 outliers final: 14 residues processed: 203 average time/residue: 0.1755 time to fit residues: 48.6948 Evaluate side-chains 179 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN B 425 ASN B 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7460 Z= 0.214 Angle : 0.566 7.788 10160 Z= 0.293 Chirality : 0.041 0.162 1200 Planarity : 0.004 0.039 1256 Dihedral : 3.462 14.022 1002 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.35 % Allowed : 12.79 % Favored : 84.86 % 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: 2.57 (0.28), residues: 940 helix: 2.37 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -0.39 (0.45), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 444 HIS 0.005 0.002 HIS A 513 PHE 0.023 0.002 PHE A 289 TYR 0.019 0.002 TYR A 134 ARG 0.010 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.7715 (mtp) cc_final: 0.7465 (mtp) REVERT: A 167 MET cc_start: 0.7724 (mmm) cc_final: 0.7468 (mmm) REVERT: A 222 PHE cc_start: 0.7188 (t80) cc_final: 0.5004 (m-10) REVERT: A 309 ARG cc_start: 0.6667 (ttp-170) cc_final: 0.5227 (mmt-90) REVERT: A 408 ARG cc_start: 0.4920 (mmp-170) cc_final: 0.4387 (tpp-160) REVERT: A 433 LEU cc_start: 0.7930 (tp) cc_final: 0.7719 (mt) REVERT: B 108 MET cc_start: 0.7781 (mtt) cc_final: 0.7473 (mtp) REVERT: B 142 VAL cc_start: 0.8580 (t) cc_final: 0.8345 (m) REVERT: B 222 PHE cc_start: 0.6670 (t80) cc_final: 0.4954 (m-80) REVERT: B 309 ARG cc_start: 0.5755 (mtm180) cc_final: 0.4964 (mmt-90) REVERT: B 395 GLU cc_start: 0.7471 (tp30) cc_final: 0.7209 (mt-10) REVERT: B 408 ARG cc_start: 0.3998 (mmm160) cc_final: 0.3524 (tpp-160) REVERT: B 477 MET cc_start: 0.7775 (ttm) cc_final: 0.7504 (ttt) REVERT: B 483 ASP cc_start: 0.6838 (t70) cc_final: 0.6473 (t0) outliers start: 18 outliers final: 13 residues processed: 191 average time/residue: 0.1696 time to fit residues: 44.8103 Evaluate side-chains 173 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7666 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7460 Z= 0.196 Angle : 0.550 7.590 10160 Z= 0.284 Chirality : 0.041 0.151 1200 Planarity : 0.004 0.038 1256 Dihedral : 3.385 13.141 1002 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.61 % Allowed : 13.97 % Favored : 83.42 % 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: 2.54 (0.28), residues: 940 helix: 2.41 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -0.59 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 444 HIS 0.006 0.002 HIS B 210 PHE 0.022 0.002 PHE A 279 TYR 0.023 0.002 TYR B 134 ARG 0.004 0.001 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6634 (ttp-170) cc_final: 0.5155 (mmt-90) REVERT: A 408 ARG cc_start: 0.5216 (mmp-170) cc_final: 0.4676 (tpp-160) REVERT: A 433 LEU cc_start: 0.7986 (tp) cc_final: 0.7717 (mt) REVERT: A 439 ILE cc_start: 0.7662 (mm) cc_final: 0.7451 (mt) REVERT: B 108 MET cc_start: 0.7820 (mtt) cc_final: 0.7548 (mtp) REVERT: B 142 VAL cc_start: 0.8580 (t) cc_final: 0.8340 (m) REVERT: B 222 PHE cc_start: 0.6609 (t80) cc_final: 0.4911 (m-80) REVERT: B 264 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 309 ARG cc_start: 0.5415 (mtm180) cc_final: 0.4544 (mmt-90) REVERT: B 395 GLU cc_start: 0.7430 (tp30) cc_final: 0.7207 (mt-10) REVERT: B 408 ARG cc_start: 0.3996 (mmm160) cc_final: 0.3409 (tpp-160) REVERT: B 477 MET cc_start: 0.7768 (ttm) cc_final: 0.7388 (ttt) REVERT: B 483 ASP cc_start: 0.6826 (t70) cc_final: 0.6063 (m-30) outliers start: 20 outliers final: 14 residues processed: 182 average time/residue: 0.1963 time to fit residues: 48.7452 Evaluate side-chains 170 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7697 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7460 Z= 0.188 Angle : 0.557 7.396 10160 Z= 0.286 Chirality : 0.041 0.163 1200 Planarity : 0.004 0.039 1256 Dihedral : 3.315 11.630 1002 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.48 % Allowed : 14.75 % Favored : 82.77 % 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: 2.52 (0.28), residues: 940 helix: 2.41 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -0.68 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 444 HIS 0.004 0.002 HIS A 513 PHE 0.021 0.002 PHE A 222 TYR 0.014 0.001 TYR A 134 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6612 (ttp-170) cc_final: 0.5080 (mmt-90) REVERT: A 349 MET cc_start: 0.6828 (tpp) cc_final: 0.6222 (ttp) REVERT: A 372 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 408 ARG cc_start: 0.5293 (mmp-170) cc_final: 0.4764 (tpp-160) REVERT: A 433 LEU cc_start: 0.8009 (tp) cc_final: 0.7785 (mt) REVERT: A 460 MET cc_start: 0.7705 (tpp) cc_final: 0.7300 (tpp) REVERT: B 108 MET cc_start: 0.7821 (mtt) cc_final: 0.7594 (mtp) REVERT: B 142 VAL cc_start: 0.8609 (t) cc_final: 0.8343 (m) REVERT: B 222 PHE cc_start: 0.6632 (t80) cc_final: 0.4941 (m-80) REVERT: B 264 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 309 ARG cc_start: 0.5467 (mtm180) cc_final: 0.4555 (mmt-90) REVERT: B 408 ARG cc_start: 0.4002 (mmm160) cc_final: 0.3508 (tpp-160) REVERT: B 477 MET cc_start: 0.7798 (ttm) cc_final: 0.7500 (ttt) REVERT: B 483 ASP cc_start: 0.6886 (t70) cc_final: 0.6151 (m-30) outliers start: 19 outliers final: 14 residues processed: 180 average time/residue: 0.1734 time to fit residues: 42.6016 Evaluate side-chains 174 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 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: 0.7749 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7460 Z= 0.198 Angle : 0.560 7.631 10160 Z= 0.288 Chirality : 0.041 0.155 1200 Planarity : 0.004 0.038 1256 Dihedral : 3.302 11.533 1002 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.00 % Allowed : 14.49 % Favored : 82.51 % 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: 2.69 (0.28), residues: 940 helix: 2.60 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.69 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 444 HIS 0.004 0.002 HIS A 513 PHE 0.019 0.002 PHE A 280 TYR 0.026 0.002 TYR B 134 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6576 (ttp-170) cc_final: 0.5029 (mmt-90) REVERT: A 349 MET cc_start: 0.6889 (tpp) cc_final: 0.6302 (ttp) REVERT: A 408 ARG cc_start: 0.5309 (mmp-170) cc_final: 0.4846 (tpp-160) REVERT: A 425 ASN cc_start: 0.7849 (t0) cc_final: 0.7479 (m-40) REVERT: A 433 LEU cc_start: 0.8084 (tp) cc_final: 0.7846 (mt) REVERT: A 460 MET cc_start: 0.7703 (tpp) cc_final: 0.7361 (tpp) REVERT: B 108 MET cc_start: 0.7879 (mtt) cc_final: 0.7650 (mtp) REVERT: B 142 VAL cc_start: 0.8631 (t) cc_final: 0.8377 (m) REVERT: B 222 PHE cc_start: 0.6490 (t80) cc_final: 0.4877 (m-80) REVERT: B 264 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 309 ARG cc_start: 0.5601 (mtm180) cc_final: 0.4787 (mmt-90) REVERT: B 408 ARG cc_start: 0.4087 (mmm160) cc_final: 0.3566 (tpp-160) REVERT: B 477 MET cc_start: 0.7839 (ttm) cc_final: 0.7529 (ttt) REVERT: B 483 ASP cc_start: 0.6968 (t70) cc_final: 0.6287 (m-30) REVERT: B 557 ILE cc_start: 0.8097 (tp) cc_final: 0.7821 (tp) outliers start: 23 outliers final: 19 residues processed: 177 average time/residue: 0.1780 time to fit residues: 42.5395 Evaluate side-chains 170 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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: 0.7780 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7460 Z= 0.201 Angle : 0.561 6.753 10160 Z= 0.290 Chirality : 0.041 0.156 1200 Planarity : 0.004 0.038 1256 Dihedral : 3.313 11.599 1002 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.13 % Allowed : 14.88 % Favored : 81.98 % 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: 2.72 (0.28), residues: 940 helix: 2.61 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 444 HIS 0.006 0.002 HIS A 513 PHE 0.023 0.002 PHE A 222 TYR 0.007 0.001 TYR A 140 ARG 0.007 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6511 (ttp-170) cc_final: 0.4912 (mmt-90) REVERT: A 349 MET cc_start: 0.7001 (tpp) cc_final: 0.6437 (ttp) REVERT: A 408 ARG cc_start: 0.5381 (mmp-170) cc_final: 0.4692 (tpp-160) REVERT: A 425 ASN cc_start: 0.7836 (t0) cc_final: 0.7502 (m-40) REVERT: A 442 LYS cc_start: 0.8818 (tppt) cc_final: 0.8566 (mmtt) REVERT: A 460 MET cc_start: 0.7759 (tpp) cc_final: 0.7454 (tpp) REVERT: B 108 MET cc_start: 0.7892 (mtt) cc_final: 0.7680 (mtp) REVERT: B 142 VAL cc_start: 0.8656 (t) cc_final: 0.8373 (m) REVERT: B 222 PHE cc_start: 0.6181 (t80) cc_final: 0.5127 (m-10) REVERT: B 264 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 309 ARG cc_start: 0.5660 (mtm180) cc_final: 0.4603 (mmt-90) REVERT: B 348 VAL cc_start: 0.8538 (t) cc_final: 0.8047 (m) REVERT: B 362 LYS cc_start: 0.7619 (mttt) cc_final: 0.7246 (mmtt) REVERT: B 408 ARG cc_start: 0.4154 (mmm160) cc_final: 0.3621 (tpp-160) REVERT: B 425 ASN cc_start: 0.7676 (t0) cc_final: 0.7293 (m-40) REVERT: B 477 MET cc_start: 0.7906 (ttm) cc_final: 0.7566 (ttt) REVERT: B 483 ASP cc_start: 0.7039 (t70) cc_final: 0.6399 (m-30) REVERT: B 557 ILE cc_start: 0.8114 (tp) cc_final: 0.7833 (tp) outliers start: 24 outliers final: 17 residues processed: 176 average time/residue: 0.1736 time to fit residues: 41.5578 Evaluate side-chains 176 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7460 Z= 0.211 Angle : 0.576 7.741 10160 Z= 0.296 Chirality : 0.042 0.220 1200 Planarity : 0.004 0.038 1256 Dihedral : 3.353 11.909 1002 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.00 % Allowed : 16.06 % Favored : 80.94 % 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: 2.62 (0.28), residues: 940 helix: 2.57 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.78 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 444 HIS 0.005 0.002 HIS A 210 PHE 0.025 0.002 PHE A 222 TYR 0.020 0.002 TYR B 134 ARG 0.006 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6544 (ttp-170) cc_final: 0.4968 (mmt-90) REVERT: A 320 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6148 (mt-10) REVERT: A 349 MET cc_start: 0.7033 (tpp) cc_final: 0.6542 (ttp) REVERT: A 408 ARG cc_start: 0.5503 (mmp-170) cc_final: 0.4782 (tpp-160) REVERT: A 425 ASN cc_start: 0.7860 (t0) cc_final: 0.7494 (m-40) REVERT: A 450 THR cc_start: 0.8072 (m) cc_final: 0.7785 (p) REVERT: A 460 MET cc_start: 0.7775 (tpp) cc_final: 0.7483 (tpp) REVERT: A 523 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7652 (mt-10) REVERT: B 142 VAL cc_start: 0.8655 (t) cc_final: 0.8382 (m) REVERT: B 222 PHE cc_start: 0.6632 (t80) cc_final: 0.4988 (m-80) REVERT: B 264 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7138 (mm-30) REVERT: B 309 ARG cc_start: 0.5695 (mtm180) cc_final: 0.4651 (mmt-90) REVERT: B 320 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6195 (mt-10) REVERT: B 348 VAL cc_start: 0.8540 (t) cc_final: 0.8079 (m) REVERT: B 362 LYS cc_start: 0.7654 (mttt) cc_final: 0.7289 (mmtt) REVERT: B 408 ARG cc_start: 0.4195 (mmm160) cc_final: 0.3613 (tpp-160) REVERT: B 425 ASN cc_start: 0.7720 (t0) cc_final: 0.7318 (m-40) REVERT: B 477 MET cc_start: 0.7954 (ttm) cc_final: 0.7592 (ttt) REVERT: B 483 ASP cc_start: 0.7076 (t70) cc_final: 0.6454 (m-30) REVERT: B 535 MET cc_start: 0.7811 (mmt) cc_final: 0.7509 (mmt) REVERT: B 557 ILE cc_start: 0.8071 (tp) cc_final: 0.7800 (tp) outliers start: 23 outliers final: 18 residues processed: 176 average time/residue: 0.1848 time to fit residues: 43.6698 Evaluate side-chains 175 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.0020 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7460 Z= 0.192 Angle : 0.589 10.139 10160 Z= 0.300 Chirality : 0.042 0.248 1200 Planarity : 0.004 0.038 1256 Dihedral : 3.341 13.381 1002 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.96 % Allowed : 17.36 % Favored : 80.68 % 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: 2.69 (0.28), residues: 940 helix: 2.65 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.85 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 444 HIS 0.004 0.001 HIS B 513 PHE 0.026 0.002 PHE A 222 TYR 0.010 0.001 TYR B 134 ARG 0.008 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.6403 (ttp-170) cc_final: 0.4901 (mmt-90) REVERT: A 317 ASP cc_start: 0.7686 (t0) cc_final: 0.7438 (t0) REVERT: A 320 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6144 (mt-10) REVERT: A 408 ARG cc_start: 0.5492 (mmp-170) cc_final: 0.4761 (tpp-160) REVERT: A 425 ASN cc_start: 0.7833 (t0) cc_final: 0.7482 (m-40) REVERT: A 450 THR cc_start: 0.8077 (m) cc_final: 0.7798 (p) REVERT: A 460 MET cc_start: 0.7796 (tpp) cc_final: 0.7501 (tpp) REVERT: B 142 VAL cc_start: 0.8652 (t) cc_final: 0.8385 (m) REVERT: B 222 PHE cc_start: 0.6732 (t80) cc_final: 0.5087 (m-10) REVERT: B 309 ARG cc_start: 0.5728 (mtm180) cc_final: 0.4658 (mmt-90) REVERT: B 348 VAL cc_start: 0.8574 (t) cc_final: 0.8096 (m) REVERT: B 362 LYS cc_start: 0.7643 (mttt) cc_final: 0.7287 (mmtt) REVERT: B 408 ARG cc_start: 0.4197 (mmm160) cc_final: 0.3808 (tpm170) REVERT: B 425 ASN cc_start: 0.7749 (t0) cc_final: 0.7339 (m-40) REVERT: B 477 MET cc_start: 0.7937 (ttm) cc_final: 0.7598 (ttt) REVERT: B 483 ASP cc_start: 0.7041 (t70) cc_final: 0.6481 (m-30) REVERT: B 523 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 535 MET cc_start: 0.7787 (mmt) cc_final: 0.7493 (mmt) REVERT: B 557 ILE cc_start: 0.8090 (tp) cc_final: 0.7845 (tp) outliers start: 15 outliers final: 15 residues processed: 168 average time/residue: 0.1845 time to fit residues: 42.1421 Evaluate side-chains 169 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 431 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7460 Z= 0.223 Angle : 0.615 9.242 10160 Z= 0.314 Chirality : 0.044 0.277 1200 Planarity : 0.005 0.042 1256 Dihedral : 3.407 13.449 1002 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.61 % Allowed : 17.10 % Favored : 80.29 % 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: 2.55 (0.28), residues: 940 helix: 2.55 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 444 HIS 0.004 0.002 HIS B 513 PHE 0.026 0.002 PHE A 222 TYR 0.025 0.001 TYR B 134 ARG 0.005 0.001 ARG A 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.7823 (ptp) cc_final: 0.7599 (ptp) REVERT: A 309 ARG cc_start: 0.6495 (ttp-170) cc_final: 0.5096 (mmt-90) REVERT: A 348 VAL cc_start: 0.8319 (t) cc_final: 0.7916 (m) REVERT: A 408 ARG cc_start: 0.5540 (mmp-170) cc_final: 0.4787 (tpp-160) REVERT: A 425 ASN cc_start: 0.7865 (t0) cc_final: 0.7484 (m-40) REVERT: A 450 THR cc_start: 0.8169 (m) cc_final: 0.7923 (p) REVERT: A 460 MET cc_start: 0.7815 (tpp) cc_final: 0.7516 (tpp) REVERT: B 142 VAL cc_start: 0.8671 (t) cc_final: 0.8402 (m) REVERT: B 222 PHE cc_start: 0.6825 (t80) cc_final: 0.5101 (m-10) REVERT: B 262 SER cc_start: 0.8723 (t) cc_final: 0.8424 (m) REVERT: B 264 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 309 ARG cc_start: 0.5840 (mtm180) cc_final: 0.4729 (mmt-90) REVERT: B 320 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6295 (mt-10) REVERT: B 348 VAL cc_start: 0.8550 (t) cc_final: 0.8092 (m) REVERT: B 362 LYS cc_start: 0.7604 (mttt) cc_final: 0.7315 (mmtt) REVERT: B 408 ARG cc_start: 0.4297 (mmm160) cc_final: 0.3921 (tpm170) REVERT: B 425 ASN cc_start: 0.7773 (t0) cc_final: 0.7361 (m-40) REVERT: B 477 MET cc_start: 0.7977 (ttm) cc_final: 0.7586 (ttt) REVERT: B 483 ASP cc_start: 0.7047 (t70) cc_final: 0.6477 (m-30) REVERT: B 523 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7627 (mt-10) REVERT: B 535 MET cc_start: 0.7826 (mmt) cc_final: 0.7568 (mmt) REVERT: B 557 ILE cc_start: 0.8127 (tp) cc_final: 0.7899 (tp) outliers start: 20 outliers final: 18 residues processed: 173 average time/residue: 0.1911 time to fit residues: 44.1282 Evaluate side-chains 172 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 516 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.164103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.133946 restraints weight = 10028.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137009 restraints weight = 6772.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138989 restraints weight = 5348.631| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7460 Z= 0.208 Angle : 0.616 11.508 10160 Z= 0.309 Chirality : 0.044 0.388 1200 Planarity : 0.004 0.039 1256 Dihedral : 3.396 13.608 1002 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.61 % Allowed : 17.75 % Favored : 79.63 % 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: 2.49 (0.28), residues: 940 helix: 2.54 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 444 HIS 0.004 0.001 HIS B 513 PHE 0.026 0.001 PHE A 222 TYR 0.011 0.001 TYR B 134 ARG 0.005 0.000 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.51 seconds wall clock time: 32 minutes 19.59 seconds (1939.59 seconds total)