Starting phenix.real_space_refine on Mon Sep 23 12:51:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/09_2024/7ypg_33999.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/09_2024/7ypg_33999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/09_2024/7ypg_33999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/09_2024/7ypg_33999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/09_2024/7ypg_33999.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/09_2024/7ypg_33999.cif" } resolution = 2.5 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1668 2.51 5 N 486 2.21 5 O 516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2676 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.92, per 1000 atoms: 0.72 Number of scatterers: 2676 At special positions: 0 Unit cell: (99.6, 110.39, 34.86, 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 6 16.00 O 516 8.00 N 486 7.00 C 1668 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: 0.58 Conformation dependent library (CDL) restraints added in 350.3 milliseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.673A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 316 through 320 Processing sheet with id=AA3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.409A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS D 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 removed outlier: 6.652A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AA6, first strand: chain 'F' and resid 308 through 310 removed outlier: 6.673A pdb=" N VAL F 309 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 316 through 320 Processing sheet with id=AA8, first strand: chain 'F' and resid 328 through 330 removed outlier: 6.410A pdb=" N HIS F 329 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 338 through 340 removed outlier: 6.651A pdb=" N GLU F 338 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 349 through 350 20 hydrogen bonds defined for protein. 60 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: 0.50 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 881 1.33 - 1.45: 217 1.45 - 1.56: 1608 1.56 - 1.67: 0 1.67 - 1.79: 6 Bond restraints: 2712 Sorted by residual: bond pdb=" CB VAL D 306 " pdb=" CG2 VAL D 306 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB VAL A 306 " pdb=" CG2 VAL A 306 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 bond pdb=" CB VAL E 306 " pdb=" CG2 VAL E 306 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL C 306 " pdb=" CG2 VAL C 306 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL F 306 " pdb=" CG2 VAL F 306 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 ... (remaining 2707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 2971 0.89 - 1.78: 534 1.78 - 2.67: 65 2.67 - 3.55: 34 3.55 - 4.44: 26 Bond angle restraints: 3630 Sorted by residual: angle pdb=" N THR A 361 " pdb=" CA THR A 361 " pdb=" C THR A 361 " ideal model delta sigma weight residual 111.17 114.75 -3.58 1.41e+00 5.03e-01 6.44e+00 angle pdb=" N THR F 361 " pdb=" CA THR F 361 " pdb=" C THR F 361 " ideal model delta sigma weight residual 111.17 114.72 -3.55 1.41e+00 5.03e-01 6.35e+00 angle pdb=" N THR D 361 " pdb=" CA THR D 361 " pdb=" C THR D 361 " ideal model delta sigma weight residual 111.17 114.71 -3.54 1.41e+00 5.03e-01 6.31e+00 angle pdb=" N THR C 361 " pdb=" CA THR C 361 " pdb=" C THR C 361 " ideal model delta sigma weight residual 111.17 114.71 -3.54 1.41e+00 5.03e-01 6.31e+00 angle pdb=" N THR E 361 " pdb=" CA THR E 361 " pdb=" C THR E 361 " ideal model delta sigma weight residual 111.17 114.70 -3.53 1.41e+00 5.03e-01 6.26e+00 ... (remaining 3625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 1506 17.74 - 35.47: 114 35.47 - 53.21: 30 53.21 - 70.95: 0 70.95 - 88.68: 6 Dihedral angle restraints: 1656 sinusoidal: 678 harmonic: 978 Sorted by residual: dihedral pdb=" CB GLU B 338 " pdb=" CG GLU B 338 " pdb=" CD GLU B 338 " pdb=" OE1 GLU B 338 " ideal model delta sinusoidal sigma weight residual 0.00 88.68 -88.68 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU D 338 " pdb=" CG GLU D 338 " pdb=" CD GLU D 338 " pdb=" OE1 GLU D 338 " ideal model delta sinusoidal sigma weight residual 0.00 88.66 -88.66 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU F 338 " pdb=" CG GLU F 338 " pdb=" CD GLU F 338 " pdb=" OE1 GLU F 338 " ideal model delta sinusoidal sigma weight residual 0.00 88.65 -88.65 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 1653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 296 0.048 - 0.095: 64 0.095 - 0.143: 36 0.143 - 0.190: 6 0.190 - 0.238: 12 Chirality restraints: 414 Sorted by residual: chirality pdb=" CB THR D 361 " pdb=" CA THR D 361 " pdb=" OG1 THR D 361 " pdb=" CG2 THR D 361 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR E 361 " pdb=" CA THR E 361 " pdb=" OG1 THR E 361 " pdb=" CG2 THR E 361 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR A 361 " pdb=" CA THR A 361 " pdb=" OG1 THR A 361 " pdb=" CG2 THR A 361 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 411 not shown) Planarity restraints: 462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 341 " -0.004 2.00e-02 2.50e+03 7.23e-03 5.22e-01 pdb=" C SER E 341 " 0.013 2.00e-02 2.50e+03 pdb=" O SER E 341 " -0.005 2.00e-02 2.50e+03 pdb=" N GLU E 342 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 341 " -0.004 2.00e-02 2.50e+03 7.11e-03 5.06e-01 pdb=" C SER B 341 " 0.012 2.00e-02 2.50e+03 pdb=" O SER B 341 " -0.005 2.00e-02 2.50e+03 pdb=" N GLU B 342 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 341 " -0.003 2.00e-02 2.50e+03 6.96e-03 4.84e-01 pdb=" C SER D 341 " 0.012 2.00e-02 2.50e+03 pdb=" O SER D 341 " -0.005 2.00e-02 2.50e+03 pdb=" N GLU D 342 " -0.004 2.00e-02 2.50e+03 ... (remaining 459 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 799 2.84 - 3.36: 2167 3.36 - 3.87: 4389 3.87 - 4.39: 4578 4.39 - 4.90: 9317 Nonbonded interactions: 21250 Sorted by model distance: nonbonded pdb=" NE2 GLN D 336 " pdb=" O GLN A 336 " model vdw 2.331 3.120 nonbonded pdb=" O GLN B 336 " pdb=" NE2 GLN A 336 " model vdw 2.343 3.120 nonbonded pdb=" O GLN D 336 " pdb=" NE2 GLN C 336 " model vdw 2.346 3.120 nonbonded pdb=" NE2 GLN B 336 " pdb=" O GLN F 336 " model vdw 2.355 3.120 nonbonded pdb=" NE2 GLN E 336 " pdb=" O GLN C 336 " model vdw 2.356 3.120 ... (remaining 21245 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 0.047 2712 Z= 0.563 Angle : 0.796 4.443 3630 Z= 0.430 Chirality : 0.064 0.238 414 Planarity : 0.003 0.007 462 Dihedral : 14.504 88.683 1032 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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: -5.97 (0.30), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.23), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.005 0.003 PHE F 346 TYR 0.009 0.003 TYR E 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.370 Fit side-chains REVERT: B 317 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7519 (mtpm) REVERT: B 343 LYS cc_start: 0.7919 (tttm) cc_final: 0.7707 (ttpt) REVERT: B 349 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6597 (mtm-85) REVERT: D 317 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7464 (mtpp) REVERT: D 340 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7541 (ttpt) REVERT: D 348 ASP cc_start: 0.7762 (m-30) cc_final: 0.7318 (m-30) REVERT: D 349 ARG cc_start: 0.6921 (mtt-85) cc_final: 0.6352 (mtp85) REVERT: D 353 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7781 (mtpp) REVERT: E 317 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7712 (mtpt) REVERT: E 340 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7644 (ttpt) REVERT: E 343 LYS cc_start: 0.7817 (tttm) cc_final: 0.7516 (ttmm) REVERT: E 349 ARG cc_start: 0.6799 (mtt-85) cc_final: 0.6325 (mtp85) REVERT: E 353 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7282 (mttm) REVERT: F 317 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7551 (mtpm) REVERT: F 348 ASP cc_start: 0.7820 (m-30) cc_final: 0.7565 (m-30) REVERT: F 349 ARG cc_start: 0.7140 (mtt-85) cc_final: 0.6885 (mtt90) REVERT: F 353 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7451 (mttp) REVERT: A 317 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7144 (mtpt) REVERT: A 349 ARG cc_start: 0.6752 (mtt-85) cc_final: 0.6532 (mtt90) REVERT: A 353 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7206 (tptt) REVERT: C 317 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7664 (tttt) REVERT: C 343 LYS cc_start: 0.7674 (tttm) cc_final: 0.7455 (tttm) REVERT: C 349 ARG cc_start: 0.6699 (mtt-85) cc_final: 0.6313 (mtt-85) REVERT: C 353 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7325 (mttp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 1.4221 time to fit residues: 117.4486 Evaluate side-chains 56 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 329 HIS B 330 HIS D 307 GLN D 329 HIS D 330 HIS E 307 GLN E 329 HIS F 307 GLN F 329 HIS F 330 HIS A 307 GLN A 329 HIS A 330 HIS C 307 GLN C 329 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2712 Z= 0.182 Angle : 0.579 4.521 3630 Z= 0.287 Chirality : 0.053 0.144 414 Planarity : 0.002 0.014 462 Dihedral : 4.155 10.510 360 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.56 % Allowed : 13.46 % Favored : 83.97 % 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: -5.54 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.003 0.001 PHE E 346 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.343 Fit side-chains REVERT: B 317 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7517 (mtpm) REVERT: B 340 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7527 (ttmm) REVERT: B 349 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6724 (mtm-85) REVERT: D 317 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7399 (ttpp) REVERT: D 340 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7604 (ttpt) REVERT: D 348 ASP cc_start: 0.7730 (m-30) cc_final: 0.7502 (m-30) REVERT: D 349 ARG cc_start: 0.6957 (mtt-85) cc_final: 0.6452 (mtp85) REVERT: D 353 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7133 (mppt) REVERT: E 317 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7557 (tttt) REVERT: E 340 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7731 (ttpt) REVERT: E 343 LYS cc_start: 0.7749 (tttm) cc_final: 0.7539 (ttmm) REVERT: E 348 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: E 349 ARG cc_start: 0.6681 (mtt-85) cc_final: 0.6311 (mtp85) REVERT: F 317 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7502 (mtpm) REVERT: F 348 ASP cc_start: 0.7804 (m-30) cc_final: 0.7557 (m-30) REVERT: F 349 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6907 (mtm-85) REVERT: F 353 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7220 (mttp) REVERT: A 340 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7663 (ttpt) REVERT: A 349 ARG cc_start: 0.6812 (mtt-85) cc_final: 0.6521 (mtt90) REVERT: A 357 LEU cc_start: 0.7996 (tt) cc_final: 0.7793 (tp) REVERT: C 317 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7590 (tttt) REVERT: C 348 ASP cc_start: 0.7798 (m-30) cc_final: 0.7525 (m-30) REVERT: C 349 ARG cc_start: 0.6660 (mtt-85) cc_final: 0.6224 (mtp-110) REVERT: C 353 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7359 (mttp) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 1.4573 time to fit residues: 106.9187 Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2712 Z= 0.200 Angle : 0.565 4.694 3630 Z= 0.277 Chirality : 0.052 0.146 414 Planarity : 0.002 0.014 462 Dihedral : 4.026 10.555 360 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.88 % Allowed : 16.99 % Favored : 80.13 % 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: -5.48 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.003 0.001 PHE E 346 TYR 0.006 0.002 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.349 Fit side-chains REVERT: B 340 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7558 (ttpp) REVERT: B 349 ARG cc_start: 0.7217 (mtt-85) cc_final: 0.6780 (mtm-85) REVERT: D 317 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7409 (ttpp) REVERT: D 340 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7511 (ttpt) REVERT: D 348 ASP cc_start: 0.7749 (m-30) cc_final: 0.7503 (m-30) REVERT: D 349 ARG cc_start: 0.6879 (mtt-85) cc_final: 0.6340 (mtp85) REVERT: D 353 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7150 (mppt) REVERT: D 358 ASP cc_start: 0.6399 (m-30) cc_final: 0.5683 (p0) REVERT: E 317 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7661 (ttpp) REVERT: E 348 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: E 349 ARG cc_start: 0.6614 (mtt-85) cc_final: 0.6255 (mtp85) REVERT: F 317 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7469 (mtpm) REVERT: F 349 ARG cc_start: 0.7205 (mtt-85) cc_final: 0.6905 (mtm-85) REVERT: A 317 LYS cc_start: 0.7553 (ttmt) cc_final: 0.7164 (mtpt) REVERT: A 349 ARG cc_start: 0.6821 (mtt-85) cc_final: 0.6415 (mtp-110) REVERT: A 357 LEU cc_start: 0.7829 (tt) cc_final: 0.7532 (tp) REVERT: C 317 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7436 (ttmm) REVERT: C 349 ARG cc_start: 0.6655 (mtt-85) cc_final: 0.6229 (mtp-110) REVERT: C 353 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7408 (mppt) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 1.5079 time to fit residues: 109.2044 Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.0370 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.9264 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2712 Z= 0.289 Angle : 0.632 5.712 3630 Z= 0.309 Chirality : 0.052 0.148 414 Planarity : 0.002 0.013 462 Dihedral : 4.480 12.852 360 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 5.45 % Allowed : 16.99 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.49 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 362 PHE 0.005 0.002 PHE E 346 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.360 Fit side-chains REVERT: B 340 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7412 (ttpp) REVERT: B 349 ARG cc_start: 0.7207 (mtt-85) cc_final: 0.6799 (mtm-85) REVERT: B 357 LEU cc_start: 0.7952 (tt) cc_final: 0.7720 (tp) REVERT: D 317 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7389 (ttpp) REVERT: D 340 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7411 (ttpt) REVERT: D 348 ASP cc_start: 0.7744 (m-30) cc_final: 0.7522 (m-30) REVERT: D 349 ARG cc_start: 0.6797 (mtt-85) cc_final: 0.6253 (mtp85) REVERT: D 353 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7203 (mppt) REVERT: E 317 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7632 (ttpp) REVERT: E 343 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7231 (tttm) REVERT: E 348 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7431 (m-30) REVERT: E 349 ARG cc_start: 0.6681 (mtt-85) cc_final: 0.6255 (mtp85) REVERT: F 317 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7412 (mtpm) REVERT: F 349 ARG cc_start: 0.7180 (mtt-85) cc_final: 0.6885 (mtm-85) REVERT: A 317 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7220 (mtpt) REVERT: A 349 ARG cc_start: 0.6762 (mtt-85) cc_final: 0.6336 (mtp-110) REVERT: A 357 LEU cc_start: 0.7986 (tt) cc_final: 0.7659 (tp) REVERT: C 317 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7436 (ttmm) REVERT: C 349 ARG cc_start: 0.6650 (mtt-85) cc_final: 0.6217 (mtp-110) REVERT: C 353 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7474 (mttp) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 1.4695 time to fit residues: 106.4118 Evaluate side-chains 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.7801 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2712 Z= 0.231 Angle : 0.584 5.169 3630 Z= 0.286 Chirality : 0.051 0.143 414 Planarity : 0.002 0.014 462 Dihedral : 4.270 11.792 360 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.41 % Allowed : 17.31 % Favored : 76.28 % 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: -5.33 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.004 0.002 PHE E 346 TYR 0.006 0.002 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.355 Fit side-chains REVERT: B 340 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7380 (ttpp) REVERT: B 349 ARG cc_start: 0.7214 (mtt-85) cc_final: 0.6839 (mtm-85) REVERT: B 353 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7403 (mtpt) REVERT: B 357 LEU cc_start: 0.7911 (tt) cc_final: 0.7673 (tp) REVERT: D 317 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7434 (ttpp) REVERT: D 340 LYS cc_start: 0.7614 (ttpt) cc_final: 0.7320 (mtmt) REVERT: D 348 ASP cc_start: 0.7756 (m-30) cc_final: 0.7528 (m-30) REVERT: D 349 ARG cc_start: 0.6818 (mtt-85) cc_final: 0.6362 (mtp85) REVERT: D 353 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7184 (mppt) REVERT: E 317 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7275 (ttmm) REVERT: E 325 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8317 (pp) REVERT: E 348 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: E 349 ARG cc_start: 0.6678 (mtt-85) cc_final: 0.6372 (mtp85) REVERT: F 317 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7460 (mtpm) REVERT: F 349 ARG cc_start: 0.7169 (mtt-85) cc_final: 0.6869 (mtm-85) REVERT: A 317 LYS cc_start: 0.7603 (ttmt) cc_final: 0.7251 (mtpt) REVERT: A 349 ARG cc_start: 0.6787 (mtt-85) cc_final: 0.6393 (mtp-110) REVERT: A 357 LEU cc_start: 0.7953 (tt) cc_final: 0.7631 (tp) REVERT: C 317 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7576 (tttt) REVERT: C 349 ARG cc_start: 0.6676 (mtt-85) cc_final: 0.6239 (mtp-110) REVERT: C 353 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7466 (mppt) outliers start: 20 outliers final: 11 residues processed: 70 average time/residue: 1.3887 time to fit residues: 99.2566 Evaluate side-chains 69 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2712 Z= 0.405 Angle : 0.712 6.346 3630 Z= 0.351 Chirality : 0.054 0.148 414 Planarity : 0.003 0.014 462 Dihedral : 4.921 14.283 360 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 6.73 % Allowed : 17.31 % Favored : 75.96 % 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: -5.56 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.006 0.003 PHE E 346 TYR 0.010 0.003 TYR C 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.356 Fit side-chains REVERT: B 340 LYS cc_start: 0.7649 (ttpt) cc_final: 0.7356 (ttpp) REVERT: B 348 ASP cc_start: 0.7899 (m-30) cc_final: 0.7486 (m-30) REVERT: B 349 ARG cc_start: 0.7243 (mtt-85) cc_final: 0.6814 (mtm-85) REVERT: B 353 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7547 (mtpt) REVERT: B 358 ASP cc_start: 0.6218 (m-30) cc_final: 0.5919 (p0) REVERT: D 317 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7446 (ttpp) REVERT: D 340 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7386 (ttpp) REVERT: D 349 ARG cc_start: 0.6813 (mtt-85) cc_final: 0.6250 (mtp85) REVERT: D 353 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7744 (mtpp) REVERT: E 317 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7591 (ttpp) REVERT: E 325 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8274 (pp) REVERT: E 348 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: E 349 ARG cc_start: 0.6744 (mtt-85) cc_final: 0.6264 (mtp85) REVERT: F 317 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7503 (mtpm) REVERT: F 349 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6888 (mtm-85) REVERT: F 353 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7221 (mttp) REVERT: A 317 LYS cc_start: 0.7539 (ttmt) cc_final: 0.7200 (mtpt) REVERT: A 349 ARG cc_start: 0.6725 (mtt-85) cc_final: 0.6290 (mtp-110) REVERT: A 357 LEU cc_start: 0.8092 (tt) cc_final: 0.7751 (tp) REVERT: C 317 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7427 (ttmm) REVERT: C 349 ARG cc_start: 0.6690 (mtt-85) cc_final: 0.6240 (mtp-110) REVERT: C 353 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7473 (mttp) outliers start: 21 outliers final: 15 residues processed: 70 average time/residue: 1.2464 time to fit residues: 89.2078 Evaluate side-chains 72 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7808 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2712 Z= 0.290 Angle : 0.636 5.668 3630 Z= 0.311 Chirality : 0.053 0.145 414 Planarity : 0.003 0.016 462 Dihedral : 4.639 12.862 360 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 5.77 % Allowed : 19.55 % Favored : 74.68 % 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: -5.46 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 362 PHE 0.004 0.002 PHE E 346 TYR 0.007 0.002 TYR C 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.350 Fit side-chains REVERT: B 340 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7386 (ttpp) REVERT: B 348 ASP cc_start: 0.7882 (m-30) cc_final: 0.7481 (m-30) REVERT: B 349 ARG cc_start: 0.7262 (mtt-85) cc_final: 0.6831 (mtm-85) REVERT: B 353 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7477 (mtpt) REVERT: D 317 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7449 (ttpp) REVERT: D 340 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7402 (ttpp) REVERT: D 349 ARG cc_start: 0.6804 (mtt-85) cc_final: 0.6277 (mtp85) REVERT: D 353 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7201 (mppt) REVERT: E 317 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7613 (ttpp) REVERT: E 325 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8238 (pp) REVERT: E 348 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: E 349 ARG cc_start: 0.6706 (mtt-85) cc_final: 0.6297 (mtp85) REVERT: F 317 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7462 (mtpm) REVERT: F 349 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6575 (mtm-85) REVERT: A 317 LYS cc_start: 0.7536 (ttmt) cc_final: 0.7200 (mtpt) REVERT: A 349 ARG cc_start: 0.6780 (mtt-85) cc_final: 0.6397 (mtp85) REVERT: A 357 LEU cc_start: 0.8007 (tt) cc_final: 0.7666 (tp) REVERT: C 317 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7587 (tttt) REVERT: C 349 ARG cc_start: 0.6704 (mtt-85) cc_final: 0.6321 (mtp-110) REVERT: C 353 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7488 (mttp) outliers start: 18 outliers final: 14 residues processed: 66 average time/residue: 1.3086 time to fit residues: 88.3219 Evaluate side-chains 71 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2712 Z= 0.215 Angle : 0.585 5.565 3630 Z= 0.283 Chirality : 0.051 0.140 414 Planarity : 0.002 0.016 462 Dihedral : 4.294 11.735 360 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.45 % Allowed : 19.87 % Favored : 74.68 % 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: -5.34 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.004 0.001 PHE E 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.352 Fit side-chains REVERT: B 340 LYS cc_start: 0.7588 (ttpt) cc_final: 0.7327 (ttpp) REVERT: B 348 ASP cc_start: 0.7896 (m-30) cc_final: 0.7493 (m-30) REVERT: B 349 ARG cc_start: 0.7263 (mtt-85) cc_final: 0.6980 (mtp85) REVERT: B 353 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7339 (mtpt) REVERT: D 317 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7478 (ttpp) REVERT: D 349 ARG cc_start: 0.6821 (mtt-85) cc_final: 0.6296 (mtp85) REVERT: D 353 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7157 (mppt) REVERT: E 317 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7228 (ttmm) REVERT: E 325 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8234 (pp) REVERT: E 348 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: E 349 ARG cc_start: 0.6695 (mtt-85) cc_final: 0.6328 (mtp-110) REVERT: F 317 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7432 (mtpm) REVERT: F 349 ARG cc_start: 0.7152 (mtt-85) cc_final: 0.6887 (mtm-85) REVERT: A 317 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7317 (mtpt) REVERT: A 349 ARG cc_start: 0.6801 (mtt-85) cc_final: 0.6497 (mtp85) REVERT: A 357 LEU cc_start: 0.7929 (tt) cc_final: 0.7583 (tp) REVERT: C 317 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7495 (ttmm) REVERT: C 349 ARG cc_start: 0.6692 (mtt-85) cc_final: 0.6323 (mtp-110) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 1.2683 time to fit residues: 85.6205 Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.0060 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2712 Z= 0.246 Angle : 0.623 6.950 3630 Z= 0.297 Chirality : 0.052 0.142 414 Planarity : 0.002 0.014 462 Dihedral : 4.393 12.069 360 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.77 % Allowed : 20.19 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.003 0.001 PHE C 346 TYR 0.006 0.002 TYR C 310 ARG 0.001 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.358 Fit side-chains REVERT: B 348 ASP cc_start: 0.7900 (m-30) cc_final: 0.7486 (m-30) REVERT: B 349 ARG cc_start: 0.7279 (mtt-85) cc_final: 0.6982 (mtp85) REVERT: B 353 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7445 (mtpt) REVERT: D 317 LYS cc_start: 0.7741 (ttmt) cc_final: 0.7468 (ttpp) REVERT: D 349 ARG cc_start: 0.6837 (mtt-85) cc_final: 0.6472 (mtp85) REVERT: D 353 LYS cc_start: 0.7892 (mtpt) cc_final: 0.7137 (mppt) REVERT: E 317 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7229 (ttmm) REVERT: E 325 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8275 (pp) REVERT: E 343 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7584 (ttpp) REVERT: E 348 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: E 349 ARG cc_start: 0.6706 (mtt-85) cc_final: 0.6418 (mtt90) REVERT: F 317 LYS cc_start: 0.7684 (ttmt) cc_final: 0.7419 (mtpm) REVERT: F 349 ARG cc_start: 0.7149 (mtt-85) cc_final: 0.6882 (mtm-85) REVERT: A 317 LYS cc_start: 0.7583 (ttmt) cc_final: 0.7262 (mtpt) REVERT: A 349 ARG cc_start: 0.6788 (mtt-85) cc_final: 0.6487 (mtp85) REVERT: A 357 LEU cc_start: 0.7982 (tt) cc_final: 0.7634 (tp) REVERT: C 317 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7483 (ttmm) REVERT: C 349 ARG cc_start: 0.6693 (mtt-85) cc_final: 0.6255 (mtp-110) outliers start: 18 outliers final: 13 residues processed: 65 average time/residue: 1.2835 time to fit residues: 85.3463 Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2712 Z= 0.251 Angle : 0.622 7.098 3630 Z= 0.298 Chirality : 0.052 0.142 414 Planarity : 0.002 0.015 462 Dihedral : 4.429 12.077 360 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.45 % Allowed : 21.15 % Favored : 73.40 % 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: -5.35 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.003 0.001 PHE C 346 TYR 0.006 0.002 TYR C 310 ARG 0.001 0.001 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.347 Fit side-chains REVERT: B 348 ASP cc_start: 0.7878 (m-30) cc_final: 0.7473 (m-30) REVERT: B 349 ARG cc_start: 0.7246 (mtt-85) cc_final: 0.6908 (mtp85) REVERT: B 353 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7439 (mtpt) REVERT: D 317 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7470 (ttpp) REVERT: D 349 ARG cc_start: 0.6846 (mtt-85) cc_final: 0.6450 (mtt-85) REVERT: D 353 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7126 (mppt) REVERT: E 317 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7230 (ttmm) REVERT: E 325 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8264 (pp) REVERT: E 343 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7546 (ttpp) REVERT: E 348 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: E 349 ARG cc_start: 0.6713 (mtt-85) cc_final: 0.6370 (mtp85) REVERT: F 317 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7420 (mtpm) REVERT: F 349 ARG cc_start: 0.7131 (mtt-85) cc_final: 0.6856 (mtm-85) REVERT: A 317 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7261 (mtpt) REVERT: A 349 ARG cc_start: 0.6774 (mtt-85) cc_final: 0.6490 (mtp85) REVERT: A 357 LEU cc_start: 0.7981 (tt) cc_final: 0.7630 (tp) REVERT: C 317 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7481 (ttmm) REVERT: C 349 ARG cc_start: 0.6693 (mtt-85) cc_final: 0.6255 (mtp-110) REVERT: C 353 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7365 (tptp) outliers start: 17 outliers final: 14 residues processed: 63 average time/residue: 1.2400 time to fit residues: 79.9955 Evaluate side-chains 68 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.138610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.111006 restraints weight = 3418.247| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.15 r_work: 0.3819 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2712 Z= 0.253 Angle : 0.627 7.088 3630 Z= 0.300 Chirality : 0.052 0.142 414 Planarity : 0.002 0.015 462 Dihedral : 4.452 12.101 360 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.77 % Allowed : 21.47 % Favored : 72.76 % 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: -5.34 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.003 0.001 PHE C 346 TYR 0.006 0.002 TYR C 310 ARG 0.001 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.26 seconds wall clock time: 34 minutes 54.20 seconds (2094.20 seconds total)