Starting phenix.real_space_refine on Fri Apr 5 20:47:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2024/7wwb_32865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2024/7wwb_32865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2024/7wwb_32865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2024/7wwb_32865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2024/7wwb_32865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwb_32865/04_2024/7wwb_32865_updated.pdb" } resolution = 3.86 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= 0.018 sd= 0.094 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 60 5.16 5 C 3682 2.51 5 N 834 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 591": "OE1" <-> "OE2" Residue "B GLU 591": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5428 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.42, per 1000 atoms: 0.63 Number of scatterers: 5428 At special positions: 0 Unit cell: (107.613, 120.657, 82.612, 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 60 16.00 O 852 8.00 N 834 7.00 C 3682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 899.2 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 30 through 50 Processing helix chain 'A' and resid 227 through 244 removed outlier: 3.553A pdb=" N ILE A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 233 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 237 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 330 removed outlier: 4.626A pdb=" N LYS A 312 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 314 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 315 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 357 removed outlier: 4.185A pdb=" N VAL A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.656A pdb=" N PHE A 342 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 415 removed outlier: 3.853A pdb=" N VAL A 390 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 391 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 392 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 407 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.578A pdb=" N SER A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE A 455 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 480 through 507 Processing helix chain 'A' and resid 511 through 524 Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 574 through 606 Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 227 through 244 removed outlier: 3.553A pdb=" N ILE B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE B 233 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B 237 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 330 removed outlier: 4.626A pdb=" N LYS B 312 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 314 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 315 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 357 removed outlier: 4.185A pdb=" N VAL B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) Proline residue: B 338 - end of helix removed outlier: 3.656A pdb=" N PHE B 342 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 350 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 415 removed outlier: 3.852A pdb=" N VAL B 390 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 391 " --> pdb=" O HIS B 388 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 392 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE B 395 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 407 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.578A pdb=" N SER B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE B 455 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 480 through 507 Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 574 through 606 392 hydrogen bonds defined for protein. 630 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: 1.43 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 756 1.30 - 1.43: 1504 1.43 - 1.56: 3180 1.56 - 1.68: 34 1.68 - 1.81: 90 Bond restraints: 5564 Sorted by residual: bond pdb=" C GLN B 337 " pdb=" O GLN B 337 " ideal model delta sigma weight residual 1.243 1.177 0.066 9.90e-03 1.02e+04 4.38e+01 bond pdb=" C GLN A 337 " pdb=" O GLN A 337 " ideal model delta sigma weight residual 1.243 1.178 0.065 9.90e-03 1.02e+04 4.35e+01 bond pdb=" C PHE B 339 " pdb=" O PHE B 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" C PHE A 339 " pdb=" O PHE A 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.25e+01 bond pdb=" C17 CLR A 702 " pdb=" C20 CLR A 702 " ideal model delta sigma weight residual 1.535 1.596 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 5559 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.09: 172 107.09 - 113.76: 3164 113.76 - 120.43: 2432 120.43 - 127.11: 1712 127.11 - 133.78: 88 Bond angle restraints: 7568 Sorted by residual: angle pdb=" C PHE B 339 " pdb=" N TRP B 340 " pdb=" CA TRP B 340 " ideal model delta sigma weight residual 120.31 109.51 10.80 1.52e+00 4.33e-01 5.05e+01 angle pdb=" C PHE A 339 " pdb=" N TRP A 340 " pdb=" CA TRP A 340 " ideal model delta sigma weight residual 120.31 109.53 10.78 1.52e+00 4.33e-01 5.03e+01 angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 113.53 107.83 5.70 9.80e-01 1.04e+00 3.38e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 113.53 107.85 5.68 9.80e-01 1.04e+00 3.36e+01 angle pdb=" C PHE B 336 " pdb=" N GLN B 337 " pdb=" CA GLN B 337 " ideal model delta sigma weight residual 120.58 128.05 -7.47 1.32e+00 5.74e-01 3.20e+01 ... (remaining 7563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3222 17.14 - 34.28: 68 34.28 - 51.42: 6 51.42 - 68.56: 4 68.56 - 85.70: 4 Dihedral angle restraints: 3304 sinusoidal: 1350 harmonic: 1954 Sorted by residual: dihedral pdb=" CA TYR B 438 " pdb=" C TYR B 438 " pdb=" N HIS B 439 " pdb=" CA HIS B 439 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 438 " pdb=" C TYR A 438 " pdb=" N HIS A 439 " pdb=" CA HIS A 439 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " pdb=" CD GLU B 591 " pdb=" OE1 GLU B 591 " ideal model delta sinusoidal sigma weight residual 0.00 -85.70 85.70 1 3.00e+01 1.11e-03 9.87e+00 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 642 0.063 - 0.125: 240 0.125 - 0.188: 32 0.188 - 0.251: 8 0.251 - 0.313: 8 Chirality restraints: 930 Sorted by residual: chirality pdb=" C13 CLR A 702 " pdb=" C12 CLR A 702 " pdb=" C14 CLR A 702 " pdb=" C17 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C14 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C15 CLR B 702 " pdb=" C8 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 927 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 343 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C PHE A 343 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 343 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 344 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 343 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C PHE B 343 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE B 343 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 344 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 493 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LEU B 493 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU B 493 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 494 " 0.013 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2831 2.99 - 3.47: 5811 3.47 - 3.94: 8562 3.94 - 4.42: 9849 4.42 - 4.90: 15171 Nonbonded interactions: 42224 Sorted by model distance: nonbonded pdb=" NZ LYS B 326 " pdb=" OD2 ASP B 619 " model vdw 2.511 2.520 nonbonded pdb=" NZ LYS A 326 " pdb=" OD2 ASP A 619 " model vdw 2.512 2.520 nonbonded pdb=" O CYS B 26 " pdb=" OG1 THR B 27 " model vdw 2.531 2.440 nonbonded pdb=" O CYS A 26 " pdb=" OG1 THR A 27 " model vdw 2.531 2.440 nonbonded pdb=" N PHE B 336 " pdb=" N GLN B 337 " model vdw 2.561 2.560 ... (remaining 42219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.650 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: 2.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.300 Find NCS groups from input model: 0.250 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.008 0.066 5564 Z= 0.527 Angle : 0.969 10.801 7568 Z= 0.650 Chirality : 0.066 0.313 930 Planarity : 0.006 0.026 860 Dihedral : 9.324 85.703 2028 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.31), residues: 642 helix: 0.69 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -2.08 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 386 HIS 0.001 0.000 HIS B 464 PHE 0.001 0.000 PHE B 348 TYR 0.001 0.000 TYR B 415 ARG 0.001 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8669 (mt) cc_final: 0.8421 (mt) REVERT: A 234 ARG cc_start: 0.7483 (ptt180) cc_final: 0.7161 (ptt-90) REVERT: A 326 LYS cc_start: 0.8897 (mttt) cc_final: 0.8603 (ttmm) REVERT: A 342 PHE cc_start: 0.7578 (t80) cc_final: 0.7357 (m-10) REVERT: A 352 TRP cc_start: 0.8852 (t60) cc_final: 0.8616 (t60) REVERT: A 354 MET cc_start: 0.8206 (mmm) cc_final: 0.7948 (tpp) REVERT: A 438 TYR cc_start: 0.7244 (m-80) cc_final: 0.7021 (m-10) REVERT: A 516 LYS cc_start: 0.6466 (mttt) cc_final: 0.6192 (mmtp) REVERT: A 528 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7031 (mpt180) REVERT: A 581 LEU cc_start: 0.8942 (mt) cc_final: 0.8654 (tt) REVERT: B 340 TRP cc_start: 0.6592 (m-10) cc_final: 0.5815 (m100) REVERT: B 437 ARG cc_start: 0.7457 (tpt90) cc_final: 0.6958 (mmt180) REVERT: B 463 ILE cc_start: 0.8796 (mt) cc_final: 0.8568 (mm) REVERT: B 508 SER cc_start: 0.8865 (m) cc_final: 0.8506 (t) REVERT: B 516 LYS cc_start: 0.6949 (mttt) cc_final: 0.6379 (mptt) REVERT: B 534 THR cc_start: 0.8810 (m) cc_final: 0.8596 (p) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1849 time to fit residues: 67.4786 Evaluate side-chains 178 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 330 HIS A 466 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5564 Z= 0.195 Angle : 0.635 7.320 7568 Z= 0.331 Chirality : 0.037 0.151 930 Planarity : 0.006 0.029 860 Dihedral : 5.103 35.715 836 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 6.38 % Allowed : 14.93 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 642 helix: 0.75 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.67 (0.53), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 386 HIS 0.002 0.001 HIS A 330 PHE 0.019 0.001 PHE B 44 TYR 0.011 0.001 TYR B 387 ARG 0.006 0.001 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8282 (ppp) cc_final: 0.8061 (ttt) REVERT: A 337 GLN cc_start: 0.8598 (tp40) cc_final: 0.8297 (tp-100) REVERT: A 342 PHE cc_start: 0.7819 (t80) cc_final: 0.7371 (m-10) REVERT: A 438 TYR cc_start: 0.7371 (m-80) cc_final: 0.7062 (m-80) REVERT: A 445 LYS cc_start: 0.8420 (tptm) cc_final: 0.8120 (tptm) REVERT: A 480 LYS cc_start: 0.8181 (mttt) cc_final: 0.7813 (mtmm) REVERT: A 516 LYS cc_start: 0.6464 (mttt) cc_final: 0.6220 (mmtp) REVERT: A 528 ARG cc_start: 0.7770 (mtt90) cc_final: 0.7158 (mpt180) REVERT: A 538 PHE cc_start: 0.8704 (t80) cc_final: 0.7809 (t80) REVERT: A 578 PHE cc_start: 0.8056 (t80) cc_final: 0.7553 (t80) REVERT: A 581 LEU cc_start: 0.8977 (mt) cc_final: 0.8609 (tt) REVERT: B 21 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7326 (pp) REVERT: B 340 TRP cc_start: 0.7081 (m-10) cc_final: 0.6666 (m-10) REVERT: B 508 SER cc_start: 0.8582 (m) cc_final: 0.8314 (t) REVERT: B 516 LYS cc_start: 0.7102 (mttt) cc_final: 0.6248 (mmtt) outliers start: 38 outliers final: 23 residues processed: 215 average time/residue: 0.1638 time to fit residues: 45.6792 Evaluate side-chains 182 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 403 GLN A 439 HIS B 439 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5564 Z= 0.180 Angle : 0.594 6.752 7568 Z= 0.305 Chirality : 0.037 0.172 930 Planarity : 0.005 0.027 860 Dihedral : 4.948 35.338 836 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.37 % Allowed : 18.12 % Favored : 76.51 % 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: 0.05 (0.32), residues: 642 helix: 0.51 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.86 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 352 HIS 0.003 0.001 HIS A 439 PHE 0.021 0.001 PHE B 48 TYR 0.017 0.001 TYR A 438 ARG 0.005 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.7995 (mmp) cc_final: 0.7552 (mmp) REVERT: A 337 GLN cc_start: 0.8784 (tp40) cc_final: 0.8583 (tp-100) REVERT: A 342 PHE cc_start: 0.7575 (t80) cc_final: 0.7146 (m-10) REVERT: A 392 LEU cc_start: 0.8388 (tp) cc_final: 0.7992 (tp) REVERT: A 403 GLN cc_start: 0.8534 (tt0) cc_final: 0.8203 (tt0) REVERT: A 516 LYS cc_start: 0.6307 (mttt) cc_final: 0.6091 (mmtp) REVERT: A 528 ARG cc_start: 0.7649 (mtt90) cc_final: 0.7133 (mpt180) REVERT: A 538 PHE cc_start: 0.8591 (t80) cc_final: 0.8159 (t80) REVERT: A 581 LEU cc_start: 0.8977 (mt) cc_final: 0.8534 (tt) REVERT: A 599 LEU cc_start: 0.8768 (tp) cc_final: 0.8386 (tp) REVERT: B 516 LYS cc_start: 0.7187 (mttt) cc_final: 0.6547 (mmtt) outliers start: 32 outliers final: 23 residues processed: 200 average time/residue: 0.1445 time to fit residues: 38.5621 Evaluate side-chains 179 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 439 HIS B 439 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5564 Z= 0.292 Angle : 0.667 6.712 7568 Z= 0.345 Chirality : 0.040 0.146 930 Planarity : 0.005 0.027 860 Dihedral : 5.771 39.517 836 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 8.22 % Allowed : 18.62 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.32), residues: 642 helix: 0.14 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.98 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 386 HIS 0.003 0.001 HIS B 330 PHE 0.019 0.002 PHE B 48 TYR 0.015 0.002 TYR A 438 ARG 0.004 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 337 GLN cc_start: 0.9026 (tp40) cc_final: 0.8822 (tp-100) REVERT: A 342 PHE cc_start: 0.7617 (t80) cc_final: 0.7289 (m-10) REVERT: A 353 ILE cc_start: 0.9491 (mm) cc_final: 0.9152 (mm) REVERT: A 480 LYS cc_start: 0.8264 (mttt) cc_final: 0.7862 (mmtt) REVERT: A 516 LYS cc_start: 0.6428 (mttt) cc_final: 0.6150 (mmtp) REVERT: A 538 PHE cc_start: 0.8676 (t80) cc_final: 0.8400 (t80) REVERT: A 581 LEU cc_start: 0.9015 (mt) cc_final: 0.8608 (tt) REVERT: B 42 MET cc_start: 0.8617 (tpt) cc_final: 0.8352 (tpp) REVERT: B 242 TRP cc_start: 0.7476 (OUTLIER) cc_final: 0.7004 (t60) REVERT: B 244 LEU cc_start: 0.9118 (tt) cc_final: 0.8825 (mm) REVERT: B 454 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8097 (ttpt) REVERT: B 516 LYS cc_start: 0.7412 (mttt) cc_final: 0.6779 (mmtt) REVERT: B 604 ASP cc_start: 0.9136 (t70) cc_final: 0.8865 (t0) outliers start: 49 outliers final: 37 residues processed: 193 average time/residue: 0.1500 time to fit residues: 38.5523 Evaluate side-chains 194 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5564 Z= 0.192 Angle : 0.594 7.204 7568 Z= 0.304 Chirality : 0.036 0.142 930 Planarity : 0.005 0.027 860 Dihedral : 5.186 32.990 836 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.88 % Allowed : 21.64 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.32), residues: 642 helix: 0.18 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.41 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 386 HIS 0.002 0.001 HIS B 388 PHE 0.023 0.001 PHE A 578 TYR 0.027 0.002 TYR A 438 ARG 0.004 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 342 PHE cc_start: 0.7618 (t80) cc_final: 0.7262 (m-10) REVERT: A 353 ILE cc_start: 0.9427 (mm) cc_final: 0.9082 (mm) REVERT: A 480 LYS cc_start: 0.8289 (mttt) cc_final: 0.7868 (mmtt) REVERT: A 581 LEU cc_start: 0.8978 (mt) cc_final: 0.8606 (tt) REVERT: A 599 LEU cc_start: 0.8883 (tp) cc_final: 0.8635 (tp) REVERT: B 40 ILE cc_start: 0.9183 (tp) cc_final: 0.8861 (tp) REVERT: B 42 MET cc_start: 0.8611 (tpt) cc_final: 0.8010 (tpp) REVERT: B 397 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8029 (mm-30) REVERT: B 454 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8124 (ttpt) REVERT: B 516 LYS cc_start: 0.7257 (mttt) cc_final: 0.6691 (mmtt) outliers start: 41 outliers final: 33 residues processed: 191 average time/residue: 0.1363 time to fit residues: 35.3319 Evaluate side-chains 192 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7864 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5564 Z= 0.178 Angle : 0.610 7.765 7568 Z= 0.312 Chirality : 0.037 0.184 930 Planarity : 0.005 0.027 860 Dihedral : 5.147 32.191 836 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.87 % Allowed : 23.49 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 642 helix: 0.24 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.46 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 352 HIS 0.002 0.001 HIS B 388 PHE 0.021 0.001 PHE A 578 TYR 0.016 0.001 TYR B 351 ARG 0.003 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8255 (ppp) cc_final: 0.8019 (ptt) REVERT: A 307 MET cc_start: 0.8566 (ppp) cc_final: 0.8320 (ttt) REVERT: A 312 LYS cc_start: 0.8093 (ttmt) cc_final: 0.7741 (tttm) REVERT: A 342 PHE cc_start: 0.7529 (t80) cc_final: 0.7220 (m-10) REVERT: A 384 MET cc_start: 0.6079 (mpp) cc_final: 0.5834 (mpp) REVERT: A 480 LYS cc_start: 0.8360 (mttt) cc_final: 0.7950 (mttt) REVERT: A 581 LEU cc_start: 0.8955 (mt) cc_final: 0.8525 (tt) REVERT: A 599 LEU cc_start: 0.8828 (tp) cc_final: 0.8445 (tp) REVERT: A 606 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8646 (ttmm) REVERT: B 29 ILE cc_start: 0.8687 (mm) cc_final: 0.8370 (mm) REVERT: B 40 ILE cc_start: 0.9137 (tp) cc_final: 0.8802 (tp) REVERT: B 42 MET cc_start: 0.8631 (tpt) cc_final: 0.8066 (tpp) REVERT: B 347 LEU cc_start: 0.9040 (mp) cc_final: 0.8601 (mp) REVERT: B 397 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8155 (mm-30) REVERT: B 454 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8149 (ttpt) REVERT: B 516 LYS cc_start: 0.7375 (mttt) cc_final: 0.6893 (mmtt) outliers start: 35 outliers final: 29 residues processed: 195 average time/residue: 0.1420 time to fit residues: 36.8281 Evaluate side-chains 192 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.0010 chunk 19 optimal weight: 5.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5564 Z= 0.158 Angle : 0.599 7.827 7568 Z= 0.305 Chirality : 0.037 0.200 930 Planarity : 0.005 0.027 860 Dihedral : 4.957 31.101 836 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.70 % Allowed : 24.83 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.33), residues: 642 helix: 0.27 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.36 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 352 HIS 0.001 0.000 HIS B 388 PHE 0.022 0.001 PHE A 538 TYR 0.015 0.001 TYR B 351 ARG 0.003 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8785 (t0) cc_final: 0.8489 (t0) REVERT: A 227 MET cc_start: 0.8229 (ppp) cc_final: 0.7963 (ptt) REVERT: A 312 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7717 (tttm) REVERT: A 342 PHE cc_start: 0.7470 (t80) cc_final: 0.7192 (m-10) REVERT: A 384 MET cc_start: 0.6028 (mpp) cc_final: 0.5811 (mpp) REVERT: A 403 GLN cc_start: 0.8376 (tt0) cc_final: 0.8047 (tt0) REVERT: A 433 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7230 (m-40) REVERT: A 464 HIS cc_start: 0.8271 (t-90) cc_final: 0.8068 (t-90) REVERT: A 480 LYS cc_start: 0.8224 (mttt) cc_final: 0.7846 (mmtt) REVERT: A 538 PHE cc_start: 0.8616 (t80) cc_final: 0.8180 (t80) REVERT: A 542 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8346 (tt) REVERT: A 581 LEU cc_start: 0.8903 (mt) cc_final: 0.8491 (tt) REVERT: A 599 LEU cc_start: 0.8734 (tp) cc_final: 0.8327 (tt) REVERT: A 606 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8703 (ttmm) REVERT: B 29 ILE cc_start: 0.8598 (mm) cc_final: 0.8312 (mm) REVERT: B 40 ILE cc_start: 0.9076 (tp) cc_final: 0.8741 (tp) REVERT: B 42 MET cc_start: 0.8713 (tpt) cc_final: 0.8095 (tpp) REVERT: B 235 TYR cc_start: 0.8076 (m-80) cc_final: 0.7718 (m-80) REVERT: B 352 TRP cc_start: 0.9422 (t60) cc_final: 0.9183 (t60) REVERT: B 388 HIS cc_start: 0.8807 (m-70) cc_final: 0.8386 (t-90) REVERT: B 397 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8088 (mm-30) REVERT: B 454 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8131 (ttpt) REVERT: B 516 LYS cc_start: 0.7361 (mttt) cc_final: 0.6856 (mmtt) REVERT: B 538 PHE cc_start: 0.7796 (t80) cc_final: 0.6753 (m-10) REVERT: B 617 TYR cc_start: 0.8670 (m-10) cc_final: 0.8437 (m-10) outliers start: 34 outliers final: 24 residues processed: 196 average time/residue: 0.1590 time to fit residues: 40.9899 Evaluate side-chains 190 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 60 optimal weight: 0.0980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5564 Z= 0.157 Angle : 0.604 7.216 7568 Z= 0.306 Chirality : 0.037 0.217 930 Planarity : 0.005 0.027 860 Dihedral : 4.888 32.655 836 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.03 % Allowed : 27.01 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.33), residues: 642 helix: 0.32 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -2.46 (0.56), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 352 HIS 0.001 0.000 HIS A 439 PHE 0.021 0.001 PHE A 538 TYR 0.014 0.001 TYR B 351 ARG 0.003 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8709 (t0) cc_final: 0.8418 (t0) REVERT: A 312 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7699 (tttm) REVERT: A 384 MET cc_start: 0.5863 (mpp) cc_final: 0.5618 (mpp) REVERT: A 403 GLN cc_start: 0.8441 (tt0) cc_final: 0.8097 (tt0) REVERT: A 464 HIS cc_start: 0.8273 (t-90) cc_final: 0.8073 (t-90) REVERT: A 480 LYS cc_start: 0.8173 (mttt) cc_final: 0.7783 (mmtt) REVERT: A 538 PHE cc_start: 0.8612 (t80) cc_final: 0.8186 (t80) REVERT: A 581 LEU cc_start: 0.8878 (mt) cc_final: 0.8463 (tt) REVERT: A 599 LEU cc_start: 0.8759 (tp) cc_final: 0.8391 (tt) REVERT: A 606 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8640 (ttmm) REVERT: B 29 ILE cc_start: 0.8702 (mm) cc_final: 0.8444 (mm) REVERT: B 40 ILE cc_start: 0.9011 (tp) cc_final: 0.8667 (tp) REVERT: B 235 TYR cc_start: 0.8069 (m-80) cc_final: 0.7715 (m-10) REVERT: B 397 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 454 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8122 (ttpt) REVERT: B 516 LYS cc_start: 0.7330 (mttt) cc_final: 0.6815 (mmtt) REVERT: B 538 PHE cc_start: 0.7648 (t80) cc_final: 0.6795 (m-10) REVERT: B 617 TYR cc_start: 0.8631 (m-10) cc_final: 0.8403 (m-10) outliers start: 30 outliers final: 25 residues processed: 192 average time/residue: 0.1376 time to fit residues: 35.2086 Evaluate side-chains 190 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5564 Z= 0.185 Angle : 0.621 7.903 7568 Z= 0.317 Chirality : 0.038 0.232 930 Planarity : 0.005 0.027 860 Dihedral : 5.042 32.879 836 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.42 % Rotamer: Outliers : 5.20 % Allowed : 27.68 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.33), residues: 642 helix: 0.29 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.65 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 352 HIS 0.001 0.000 HIS B 330 PHE 0.021 0.001 PHE A 343 TYR 0.012 0.001 TYR A 235 ARG 0.003 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8694 (t0) cc_final: 0.8454 (t0) REVERT: A 312 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7730 (tttm) REVERT: A 464 HIS cc_start: 0.8280 (t-90) cc_final: 0.8077 (t-90) REVERT: A 480 LYS cc_start: 0.8165 (mttt) cc_final: 0.7810 (mmtt) REVERT: A 581 LEU cc_start: 0.8925 (mt) cc_final: 0.8501 (tt) REVERT: A 599 LEU cc_start: 0.8868 (tp) cc_final: 0.8324 (tt) REVERT: B 29 ILE cc_start: 0.8726 (mm) cc_final: 0.8452 (mm) REVERT: B 40 ILE cc_start: 0.8955 (tp) cc_final: 0.8620 (tp) REVERT: B 42 MET cc_start: 0.8651 (tpt) cc_final: 0.8304 (tpp) REVERT: B 235 TYR cc_start: 0.8026 (m-80) cc_final: 0.7720 (m-80) REVERT: B 454 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8318 (ttmt) REVERT: B 516 LYS cc_start: 0.7403 (mttt) cc_final: 0.6922 (mmtt) REVERT: B 538 PHE cc_start: 0.7622 (t80) cc_final: 0.6780 (m-10) REVERT: B 617 TYR cc_start: 0.8622 (m-10) cc_final: 0.8349 (m-10) outliers start: 31 outliers final: 28 residues processed: 182 average time/residue: 0.1455 time to fit residues: 35.0492 Evaluate side-chains 186 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.0470 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5564 Z= 0.162 Angle : 0.622 8.009 7568 Z= 0.315 Chirality : 0.037 0.203 930 Planarity : 0.005 0.027 860 Dihedral : 4.870 33.351 836 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.36 % Allowed : 28.19 % Favored : 67.45 % 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: -0.26 (0.33), residues: 642 helix: 0.32 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -2.36 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 352 HIS 0.001 0.000 HIS A 584 PHE 0.023 0.001 PHE A 343 TYR 0.013 0.001 TYR A 351 ARG 0.003 0.000 ARG B 614 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7661 (tttm) REVERT: A 403 GLN cc_start: 0.8420 (tt0) cc_final: 0.8081 (tt0) REVERT: A 405 MET cc_start: 0.8711 (tpp) cc_final: 0.8481 (tpp) REVERT: A 538 PHE cc_start: 0.8549 (t80) cc_final: 0.8001 (t80) REVERT: A 581 LEU cc_start: 0.8870 (mt) cc_final: 0.8436 (tt) REVERT: A 599 LEU cc_start: 0.8688 (tp) cc_final: 0.8294 (tt) REVERT: B 29 ILE cc_start: 0.8670 (mm) cc_final: 0.8430 (mm) REVERT: B 40 ILE cc_start: 0.8962 (tp) cc_final: 0.8656 (tp) REVERT: B 42 MET cc_start: 0.8621 (tpt) cc_final: 0.8315 (tpp) REVERT: B 235 TYR cc_start: 0.7993 (m-80) cc_final: 0.7732 (m-80) REVERT: B 397 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 438 TYR cc_start: 0.7662 (m-80) cc_final: 0.7444 (m-10) REVERT: B 454 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8205 (ttmt) REVERT: B 516 LYS cc_start: 0.7469 (mttt) cc_final: 0.6965 (mmtt) REVERT: B 538 PHE cc_start: 0.7550 (t80) cc_final: 0.6787 (m-10) REVERT: B 617 TYR cc_start: 0.8563 (m-10) cc_final: 0.8294 (m-10) outliers start: 26 outliers final: 23 residues processed: 179 average time/residue: 0.1376 time to fit residues: 32.9734 Evaluate side-chains 184 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.0770 chunk 35 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120382 restraints weight = 9234.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120614 restraints weight = 6767.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122145 restraints weight = 5944.115| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.7941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5564 Z= 0.192 Angle : 0.643 7.638 7568 Z= 0.329 Chirality : 0.038 0.242 930 Planarity : 0.005 0.026 860 Dihedral : 5.033 34.469 836 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 4.53 % Allowed : 27.52 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.33), residues: 642 helix: 0.30 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -2.17 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 352 HIS 0.003 0.001 HIS B 388 PHE 0.023 0.001 PHE A 343 TYR 0.012 0.001 TYR A 235 ARG 0.003 0.000 ARG B 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1408.57 seconds wall clock time: 26 minutes 19.57 seconds (1579.57 seconds total)