Starting phenix.real_space_refine on Sun Mar 10 15:11:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/03_2024/7ypg_33999.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/03_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_33999/03_2024/7ypg_33999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/03_2024/7ypg_33999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/03_2024/7ypg_33999.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/03_2024/7ypg_33999.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2676 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "E" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} 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} Chain: "C" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Time building chain proxies: 1.93, 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 - 3.50 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: 1.03 Conformation dependent library (CDL) restraints added in 528.0 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: 0.25 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: 0.44 Time building geometry restraints manager: 1.11 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: 102.01 - 107.85: 174 107.85 - 113.69: 1532 113.69 - 119.53: 627 119.53 - 125.37: 1266 125.37 - 131.21: 31 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 2.520 nonbonded pdb=" O GLN B 336 " pdb=" NE2 GLN A 336 " model vdw 2.343 2.520 nonbonded pdb=" O GLN D 336 " pdb=" NE2 GLN C 336 " model vdw 2.346 2.520 nonbonded pdb=" NE2 GLN B 336 " pdb=" O GLN F 336 " model vdw 2.355 2.520 nonbonded pdb=" NE2 GLN E 336 " pdb=" O GLN C 336 " model vdw 2.356 2.520 ... (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 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: 1.130 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: 5.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- 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 : 0.320 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: 1.3934 time to fit residues: 115.0018 Evaluate side-chains 56 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7822 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2712 Z= 0.191 Angle : 0.585 4.730 3630 Z= 0.287 Chirality : 0.052 0.145 414 Planarity : 0.002 0.012 462 Dihedral : 4.236 11.660 360 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.92 % Allowed : 14.10 % 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 : -4.22 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.004 0.001 PHE F 346 TYR 0.004 0.001 TYR A 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: 6 poor density : 71 time to evaluate : 0.340 Fit side-chains REVERT: B 317 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7504 (mtpm) REVERT: B 347 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7784 (mtpm) REVERT: B 349 ARG cc_start: 0.7199 (mtt-85) cc_final: 0.6755 (mtm-85) REVERT: D 317 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7369 (ttpp) REVERT: D 340 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7519 (ttpt) REVERT: D 348 ASP cc_start: 0.7716 (m-30) cc_final: 0.7489 (m-30) REVERT: D 349 ARG cc_start: 0.6950 (mtt-85) cc_final: 0.6375 (mtp85) REVERT: D 353 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7145 (mppt) REVERT: E 317 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7695 (mtpt) REVERT: E 340 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7560 (ttpt) REVERT: E 343 LYS cc_start: 0.7740 (tttm) cc_final: 0.7499 (ttmm) REVERT: E 348 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: E 349 ARG cc_start: 0.6674 (mtt-85) cc_final: 0.6284 (mtp85) REVERT: E 353 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7535 (tttm) REVERT: F 317 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7484 (mtpm) REVERT: F 340 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7519 (ttpp) REVERT: F 348 ASP cc_start: 0.7795 (m-30) cc_final: 0.7523 (m-30) REVERT: F 349 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6926 (mtm-85) REVERT: F 353 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7248 (mttp) REVERT: A 349 ARG cc_start: 0.6800 (mtt-85) cc_final: 0.6512 (mtt90) REVERT: A 353 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7167 (tptt) REVERT: A 357 LEU cc_start: 0.8001 (tt) cc_final: 0.7779 (tp) REVERT: C 317 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7604 (tttt) REVERT: C 348 ASP cc_start: 0.7792 (m-30) cc_final: 0.7496 (m-30) REVERT: C 349 ARG cc_start: 0.6668 (mtt-85) cc_final: 0.6229 (mtp-110) REVERT: C 353 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7547 (tptp) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 1.3902 time to fit residues: 103.5082 Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2712 Z= 0.407 Angle : 0.736 6.881 3630 Z= 0.360 Chirality : 0.054 0.154 414 Planarity : 0.003 0.015 462 Dihedral : 4.978 14.243 360 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 5.77 % Allowed : 14.74 % Favored : 79.49 % 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: -5.82 (0.30), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.23), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.007 0.003 PHE E 346 TYR 0.010 0.003 TYR C 310 ARG 0.003 0.001 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 83 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 0.335 Fit side-chains REVERT: B 348 ASP cc_start: 0.7889 (m-30) cc_final: 0.7494 (m-30) REVERT: B 349 ARG cc_start: 0.7263 (mtt-85) cc_final: 0.6819 (mtm-85) REVERT: D 317 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7404 (ttpp) REVERT: D 340 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7436 (ttpt) REVERT: D 349 ARG cc_start: 0.6805 (mtt-85) cc_final: 0.6234 (mtp85) REVERT: D 353 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7698 (mtpp) REVERT: E 317 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7625 (ttpp) REVERT: E 348 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: E 349 ARG cc_start: 0.6707 (mtt-85) cc_final: 0.6287 (mtp85) REVERT: E 353 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7102 (mptp) REVERT: F 317 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7477 (mtpm) REVERT: F 340 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7503 (ttpp) REVERT: F 348 ASP cc_start: 0.7850 (m-30) cc_final: 0.7647 (m-30) REVERT: F 349 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6946 (mtm-85) REVERT: F 353 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7323 (mttp) REVERT: F 358 ASP cc_start: 0.6227 (m-30) cc_final: 0.6024 (m-30) REVERT: A 317 LYS cc_start: 0.7546 (ttmt) cc_final: 0.7172 (mtpt) REVERT: A 349 ARG cc_start: 0.6774 (mtt-85) cc_final: 0.6317 (mtp-110) REVERT: A 357 LEU cc_start: 0.8055 (tt) cc_final: 0.7665 (tp) REVERT: C 317 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7434 (ttmm) REVERT: C 349 ARG cc_start: 0.6677 (mtt-85) cc_final: 0.6268 (mtp-110) outliers start: 18 outliers final: 14 residues processed: 76 average time/residue: 1.3153 time to fit residues: 102.0872 Evaluate side-chains 75 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU 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 Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C 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: 9.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2712 Z= 0.377 Angle : 0.707 6.429 3630 Z= 0.348 Chirality : 0.054 0.150 414 Planarity : 0.003 0.015 462 Dihedral : 4.994 15.036 360 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 8.65 % Allowed : 15.06 % 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: -5.75 (0.30), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.23), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.007 0.003 PHE E 346 TYR 0.009 0.003 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 86 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 59 time to evaluate : 0.346 Fit side-chains REVERT: B 348 ASP cc_start: 0.7879 (m-30) cc_final: 0.7480 (m-30) REVERT: B 349 ARG cc_start: 0.7234 (mtt-85) cc_final: 0.6786 (mtm-85) REVERT: B 353 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7566 (mtpt) REVERT: D 317 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7429 (ttpp) REVERT: D 349 ARG cc_start: 0.6820 (mtt-85) cc_final: 0.6303 (mtp85) REVERT: D 353 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7709 (mtpp) REVERT: E 317 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7625 (ttpp) REVERT: E 325 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8375 (pp) REVERT: E 348 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: E 349 ARG cc_start: 0.6747 (mtt-85) cc_final: 0.6290 (mtp85) REVERT: E 353 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7082 (mptp) REVERT: F 317 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7531 (mtpm) REVERT: F 349 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6894 (mtm-85) REVERT: F 353 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7222 (mttp) REVERT: A 317 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7223 (mtpt) REVERT: A 349 ARG cc_start: 0.6782 (mtt-85) cc_final: 0.6328 (mtp-110) REVERT: A 357 LEU cc_start: 0.8080 (tt) cc_final: 0.7689 (tp) REVERT: C 317 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7412 (ttmm) REVERT: C 349 ARG cc_start: 0.6738 (mtt-85) cc_final: 0.6375 (mtp-110) outliers start: 27 outliers final: 20 residues processed: 77 average time/residue: 1.1887 time to fit residues: 93.6727 Evaluate side-chains 82 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 59 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU 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 D residue 348 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E 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 347 LYS Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 320 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 Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2712 Z= 0.192 Angle : 0.569 4.669 3630 Z= 0.278 Chirality : 0.051 0.139 414 Planarity : 0.002 0.016 462 Dihedral : 4.260 12.787 360 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.09 % Allowed : 19.23 % 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: -5.45 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.24), 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 0.004 0.001 TYR A 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 78 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 0.285 Fit side-chains REVERT: B 340 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7259 (ttpp) REVERT: B 348 ASP cc_start: 0.7911 (m-30) cc_final: 0.7490 (m-30) REVERT: B 349 ARG cc_start: 0.7255 (mtt-85) cc_final: 0.6859 (mtm-85) REVERT: D 317 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7440 (ttpp) REVERT: D 349 ARG cc_start: 0.6827 (mtt-85) cc_final: 0.6401 (mtp85) REVERT: D 353 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7200 (mppt) REVERT: E 317 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7287 (ttmm) REVERT: E 325 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8312 (pp) REVERT: E 348 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: E 349 ARG cc_start: 0.6688 (mtt-85) cc_final: 0.6387 (mtp85) REVERT: E 353 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7552 (ttpp) REVERT: F 317 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7449 (mtpm) REVERT: F 349 ARG cc_start: 0.7171 (mtt-85) cc_final: 0.6876 (mtm-85) REVERT: A 317 LYS cc_start: 0.7609 (ttmt) cc_final: 0.7110 (mttt) REVERT: A 349 ARG cc_start: 0.6786 (mtt-85) cc_final: 0.6391 (mtp-110) REVERT: A 357 LEU cc_start: 0.7959 (tt) cc_final: 0.7654 (tp) REVERT: C 317 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7434 (ttmm) REVERT: C 349 ARG cc_start: 0.6707 (mtt-85) cc_final: 0.6343 (mtp-110) outliers start: 19 outliers final: 11 residues processed: 71 average time/residue: 1.2564 time to fit residues: 91.1406 Evaluate side-chains 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E 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 348 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.2740 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= 0.207 Angle : 0.575 5.021 3630 Z= 0.279 Chirality : 0.051 0.141 414 Planarity : 0.002 0.016 462 Dihedral : 4.185 12.242 360 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.73 % Allowed : 19.87 % 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 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.24), 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 0.001 TYR A 310 ARG 0.001 0.000 ARG E 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 74 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.324 Fit side-chains REVERT: B 340 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7208 (ttpp) REVERT: B 348 ASP cc_start: 0.7920 (m-30) cc_final: 0.7498 (m-30) REVERT: B 349 ARG cc_start: 0.7272 (mtt-85) cc_final: 0.6883 (mtm-85) REVERT: B 353 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7415 (mtpt) REVERT: D 317 LYS cc_start: 0.7725 (ttmt) cc_final: 0.7460 (ttpp) REVERT: D 349 ARG cc_start: 0.6811 (mtt-85) cc_final: 0.6384 (mtp85) REVERT: D 353 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7211 (mppt) REVERT: E 317 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7286 (ttmm) REVERT: E 325 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8282 (pp) REVERT: E 343 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7277 (tttm) REVERT: E 348 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: E 349 ARG cc_start: 0.6712 (mtt-85) cc_final: 0.6367 (mtp85) REVERT: E 353 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7555 (ttpp) REVERT: F 317 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7476 (mtpm) REVERT: A 317 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7136 (mttt) REVERT: A 349 ARG cc_start: 0.6775 (mtt-85) cc_final: 0.6383 (mtp-110) REVERT: A 357 LEU cc_start: 0.7924 (tt) cc_final: 0.7622 (tp) REVERT: C 317 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7440 (ttmm) REVERT: C 349 ARG cc_start: 0.6668 (mtt-85) cc_final: 0.6311 (mtp-110) outliers start: 21 outliers final: 14 residues processed: 66 average time/residue: 1.2763 time to fit residues: 86.1031 Evaluate side-chains 70 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 318 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 316 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2712 Z= 0.331 Angle : 0.663 6.113 3630 Z= 0.323 Chirality : 0.053 0.146 414 Planarity : 0.003 0.013 462 Dihedral : 4.718 13.512 360 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 7.05 % Allowed : 20.83 % Favored : 72.12 % 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 0.006 0.002 PHE E 346 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.001 ARG A 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 77 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 55 time to evaluate : 0.337 Fit side-chains REVERT: B 348 ASP cc_start: 0.7854 (m-30) cc_final: 0.7431 (m-30) REVERT: B 349 ARG cc_start: 0.7252 (mtt-85) cc_final: 0.6847 (mtm-85) REVERT: B 353 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7528 (mtpt) REVERT: D 317 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7483 (ttpp) REVERT: D 349 ARG cc_start: 0.6832 (mtt-85) cc_final: 0.6307 (mtp85) REVERT: D 353 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7111 (mppt) REVERT: E 317 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7272 (ttmm) REVERT: E 325 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8290 (pp) REVERT: E 348 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: E 349 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6256 (mtp85) REVERT: E 353 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7068 (mptp) REVERT: F 317 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7514 (mtpm) REVERT: A 317 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7311 (mtpt) REVERT: A 349 ARG cc_start: 0.6616 (mtt-85) cc_final: 0.6280 (mtp-110) REVERT: A 357 LEU cc_start: 0.8048 (tt) cc_final: 0.7675 (tp) REVERT: C 317 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7464 (ttmm) REVERT: C 349 ARG cc_start: 0.6728 (mtt-85) cc_final: 0.6325 (mtp-110) outliers start: 22 outliers final: 17 residues processed: 70 average time/residue: 1.2016 time to fit residues: 86.0926 Evaluate side-chains 72 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 318 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 348 ASP Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2712 Z= 0.139 Angle : 0.545 5.627 3630 Z= 0.260 Chirality : 0.050 0.134 414 Planarity : 0.002 0.017 462 Dihedral : 3.811 11.273 360 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.53 % Allowed : 24.04 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.002 0.001 PHE E 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG E 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 72 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.343 Fit side-chains REVERT: B 349 ARG cc_start: 0.7261 (mtt-85) cc_final: 0.6810 (mtm-85) REVERT: D 317 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7456 (ttpp) REVERT: D 349 ARG cc_start: 0.6836 (mtt-85) cc_final: 0.6398 (mtp85) REVERT: D 353 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7229 (mptt) REVERT: E 317 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7606 (tttt) REVERT: E 343 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7225 (tmtm) REVERT: E 348 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: E 349 ARG cc_start: 0.6604 (mtt-85) cc_final: 0.6255 (mtp85) REVERT: E 353 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7557 (ttpp) REVERT: F 317 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7482 (mtpm) REVERT: A 317 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7217 (mttt) REVERT: A 340 LYS cc_start: 0.7343 (ttpt) cc_final: 0.7074 (ttpp) REVERT: A 349 ARG cc_start: 0.6774 (mtt-85) cc_final: 0.6351 (mtp85) REVERT: A 357 LEU cc_start: 0.7834 (tt) cc_final: 0.7541 (tp) REVERT: C 317 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7417 (ttmm) REVERT: C 348 ASP cc_start: 0.7671 (m-30) cc_final: 0.7394 (m-30) REVERT: C 349 ARG cc_start: 0.6624 (mtt-85) cc_final: 0.6252 (mtp85) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 1.3145 time to fit residues: 89.9913 Evaluate side-chains 63 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain E residue 318 VAL 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 316 SER Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2712 Z= 0.355 Angle : 0.679 6.951 3630 Z= 0.328 Chirality : 0.053 0.145 414 Planarity : 0.003 0.015 462 Dihedral : 4.667 13.311 360 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 5.45 % Allowed : 22.76 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.006 0.002 PHE E 346 TYR 0.009 0.003 TYR D 310 ARG 0.003 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: 17 poor density : 53 time to evaluate : 0.263 Fit side-chains REVERT: B 348 ASP cc_start: 0.7860 (m-30) cc_final: 0.7440 (m-30) REVERT: B 349 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6933 (mtp85) REVERT: B 353 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7524 (mtpt) REVERT: D 317 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7474 (ttpp) REVERT: D 349 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.6234 (mtt-85) REVERT: D 353 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7184 (mppt) REVERT: E 317 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7279 (ttmm) REVERT: E 325 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8259 (pp) REVERT: E 343 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7279 (tmtm) REVERT: E 348 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: E 349 ARG cc_start: 0.6702 (mtt-85) cc_final: 0.6224 (mtp85) REVERT: E 353 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7214 (mppt) REVERT: F 317 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7472 (mtpm) REVERT: A 317 LYS cc_start: 0.7594 (ttmt) cc_final: 0.7144 (mttt) REVERT: A 349 ARG cc_start: 0.6610 (mtt-85) cc_final: 0.6300 (mtp-110) REVERT: A 357 LEU cc_start: 0.8005 (tt) cc_final: 0.7686 (tp) REVERT: C 317 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7470 (ttmm) REVERT: C 349 ARG cc_start: 0.6684 (mtt-85) cc_final: 0.6223 (mtp-110) outliers start: 17 outliers final: 13 residues processed: 62 average time/residue: 1.3819 time to fit residues: 87.4611 Evaluate side-chains 68 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 318 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 316 SER Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.2881 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= 0.246 Angle : 0.630 7.299 3630 Z= 0.300 Chirality : 0.052 0.143 414 Planarity : 0.003 0.015 462 Dihedral : 4.455 12.588 360 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.49 % Allowed : 23.72 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (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 C 346 TYR 0.006 0.002 TYR D 310 ARG 0.002 0.001 ARG A 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 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.346 Fit side-chains REVERT: B 348 ASP cc_start: 0.7885 (m-30) cc_final: 0.7448 (m-30) REVERT: B 349 ARG cc_start: 0.7245 (mtt-85) cc_final: 0.6945 (mtp85) REVERT: B 353 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7495 (mtpt) REVERT: B 357 LEU cc_start: 0.8078 (tt) cc_final: 0.7818 (tp) REVERT: D 317 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7468 (ttpp) REVERT: D 349 ARG cc_start: 0.6830 (mtt-85) cc_final: 0.6399 (mtp85) REVERT: D 353 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7222 (mppt) REVERT: E 317 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7259 (ttmm) REVERT: E 325 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8225 (pp) REVERT: E 343 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7226 (tmtm) REVERT: E 348 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: E 349 ARG cc_start: 0.6721 (mtt-85) cc_final: 0.6476 (mtt90) REVERT: E 353 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7517 (ttpp) REVERT: F 317 LYS cc_start: 0.7749 (ttmt) cc_final: 0.7469 (mtpm) REVERT: A 317 LYS cc_start: 0.7579 (ttmt) cc_final: 0.7141 (mttt) REVERT: A 343 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7361 (tttm) REVERT: A 349 ARG cc_start: 0.6672 (mtt-85) cc_final: 0.6413 (mtp85) REVERT: A 357 LEU cc_start: 0.7936 (tt) cc_final: 0.7621 (tp) REVERT: C 317 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7453 (ttmm) REVERT: C 349 ARG cc_start: 0.6708 (mtt-85) cc_final: 0.6252 (mtp-110) outliers start: 14 outliers final: 11 residues processed: 60 average time/residue: 1.3086 time to fit residues: 80.2680 Evaluate side-chains 68 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 348 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 318 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 343 LYS Chi-restraints excluded: chain A residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.135897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.109057 restraints weight = 3568.307| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.16 r_work: 0.3806 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2712 Z= 0.304 Angle : 0.660 7.098 3630 Z= 0.316 Chirality : 0.053 0.144 414 Planarity : 0.003 0.015 462 Dihedral : 4.607 13.035 360 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 6.09 % Allowed : 22.12 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.25), 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 0.008 0.002 TYR D 310 ARG 0.002 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.76 seconds wall clock time: 33 minutes 53.70 seconds (2033.70 seconds total)