Starting phenix.real_space_refine on Mon Sep 30 03:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/09_2024/8jma_36411_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/09_2024/8jma_36411.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/8jma_36411/09_2024/8jma_36411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/09_2024/8jma_36411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/09_2024/8jma_36411_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jma_36411/09_2024/8jma_36411_neut_trim.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= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7848 2.51 5 N 2056 2.21 5 O 2120 1.98 5 H 12472 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24568 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 14.75, per 1000 atoms: 0.60 Number of scatterers: 24568 At special positions: 0 Unit cell: (110.67, 110.67, 105.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2120 8.00 N 2056 7.00 C 7848 6.00 H 12472 1.00 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: 6.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 85.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.550A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.509A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.068A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.764A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.945A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.708A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 73 through 100 removed outlier: 3.550A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.509A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.068A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 368 removed outlier: 3.764A pdb=" N ILE B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.945A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.710A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.550A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.509A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.068A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 368 removed outlier: 3.763A pdb=" N ILE C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.945A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.708A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.550A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.509A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.068A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 368 removed outlier: 3.764A pdb=" N ILE D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.945A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.708A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.635A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.635A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.635A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.635A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3204 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: 8.86 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12440 1.02 - 1.21: 32 1.21 - 1.41: 5022 1.41 - 1.61: 7194 1.61 - 1.81: 112 Bond restraints: 24800 Sorted by residual: bond pdb=" C2 FRU C 501 " pdb=" O5 FRU C 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C2 FRU B 501 " pdb=" O5 FRU B 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C2 FRU D 501 " pdb=" O5 FRU D 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C2 FRU A 501 " pdb=" O5 FRU A 501 " ideal model delta sigma weight residual 1.412 1.483 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 FRU B 501 " pdb=" O5 FRU B 501 " ideal model delta sigma weight residual 1.420 1.486 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 24795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 42733 1.16 - 2.33: 1910 2.33 - 3.49: 106 3.49 - 4.65: 31 4.65 - 5.81: 12 Bond angle restraints: 44792 Sorted by residual: angle pdb=" C ILE A 418 " pdb=" CA ILE A 418 " pdb=" CB ILE A 418 " ideal model delta sigma weight residual 112.02 107.82 4.20 1.31e+00 5.83e-01 1.03e+01 angle pdb=" C ILE D 418 " pdb=" CA ILE D 418 " pdb=" CB ILE D 418 " ideal model delta sigma weight residual 112.02 107.85 4.17 1.31e+00 5.83e-01 1.01e+01 angle pdb=" C ILE C 418 " pdb=" CA ILE C 418 " pdb=" CB ILE C 418 " ideal model delta sigma weight residual 112.02 107.87 4.15 1.31e+00 5.83e-01 1.00e+01 angle pdb=" C ILE B 418 " pdb=" CA ILE B 418 " pdb=" CB ILE B 418 " ideal model delta sigma weight residual 112.02 107.91 4.11 1.31e+00 5.83e-01 9.86e+00 angle pdb=" C VAL A 417 " pdb=" CA VAL A 417 " pdb=" CB VAL A 417 " ideal model delta sigma weight residual 112.14 108.36 3.78 1.35e+00 5.49e-01 7.85e+00 ... (remaining 44787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 10306 17.25 - 34.50: 910 34.50 - 51.75: 220 51.75 - 69.00: 160 69.00 - 86.25: 8 Dihedral angle restraints: 11604 sinusoidal: 6272 harmonic: 5332 Sorted by residual: dihedral pdb=" CB GLU B 66 " pdb=" CG GLU B 66 " pdb=" CD GLU B 66 " pdb=" OE1 GLU B 66 " ideal model delta sinusoidal sigma weight residual 0.00 86.25 -86.25 1 3.00e+01 1.11e-03 9.97e+00 dihedral pdb=" CB GLU A 66 " pdb=" CG GLU A 66 " pdb=" CD GLU A 66 " pdb=" OE1 GLU A 66 " ideal model delta sinusoidal sigma weight residual 0.00 86.20 -86.20 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CB GLU D 66 " pdb=" CG GLU D 66 " pdb=" CD GLU D 66 " pdb=" OE1 GLU D 66 " ideal model delta sinusoidal sigma weight residual 0.00 86.20 -86.20 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 11601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1212 0.025 - 0.050: 474 0.050 - 0.075: 252 0.075 - 0.100: 50 0.100 - 0.125: 24 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA ILE A 3 " pdb=" N ILE A 3 " pdb=" C ILE A 3 " pdb=" CB ILE A 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 3 " pdb=" N ILE B 3 " pdb=" C ILE B 3 " pdb=" CB ILE B 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE D 3 " pdb=" N ILE D 3 " pdb=" C ILE D 3 " pdb=" CB ILE D 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 2009 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 413 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ALA A 413 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 413 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 414 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 413 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ALA D 413 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA D 413 " 0.015 2.00e-02 2.50e+03 pdb=" N THR D 414 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 413 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ALA B 413 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 413 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 414 " -0.013 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1675 2.21 - 2.80: 52319 2.80 - 3.40: 73625 3.40 - 4.00: 94551 4.00 - 4.60: 147383 Nonbonded interactions: 369553 Sorted by model distance: nonbonded pdb=" OD1 ASN A 401 " pdb=" HG1 THR A 403 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASN D 401 " pdb=" HG1 THR D 403 " model vdw 1.608 2.450 nonbonded pdb=" OD1 ASN B 401 " pdb=" HG1 THR B 403 " model vdw 1.608 2.450 nonbonded pdb=" OD1 ASN C 401 " pdb=" HG1 THR C 403 " model vdw 1.608 2.450 nonbonded pdb=" H ASN C 27 " pdb=" O ARG C 31 " model vdw 1.615 2.450 ... (remaining 369548 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' } 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: 0.700 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: 0.380 Extract box with map and model: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 52.340 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 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:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.004 0.071 12328 Z= 0.290 Angle : 0.512 5.813 16728 Z= 0.282 Chirality : 0.035 0.125 2012 Planarity : 0.004 0.022 2040 Dihedral : 16.386 86.254 4472 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 17.93 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.21), residues: 1508 helix: 2.43 (0.14), residues: 1264 sheet: 1.30 (0.74), residues: 48 loop : -0.65 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 328 HIS 0.003 0.001 HIS C 337 PHE 0.011 0.001 PHE A 298 TYR 0.007 0.001 TYR A 415 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.873 Fit side-chains REVERT: A 33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7336 (mp0) REVERT: B 33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7335 (mp0) REVERT: C 33 GLU cc_start: 0.7562 (mp0) cc_final: 0.7333 (mp0) REVERT: D 33 GLU cc_start: 0.7559 (mp0) cc_final: 0.7334 (mp0) outliers start: 8 outliers final: 8 residues processed: 168 average time/residue: 2.5563 time to fit residues: 469.6990 Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 423 GLN B 383 GLN B 423 GLN C 383 GLN C 423 GLN D 383 GLN D 423 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12328 Z= 0.230 Angle : 0.465 4.022 16728 Z= 0.258 Chirality : 0.035 0.132 2012 Planarity : 0.003 0.030 2040 Dihedral : 4.328 25.693 1764 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.52 % Allowed : 16.72 % Favored : 81.76 % 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: 3.46 (0.21), residues: 1508 helix: 2.73 (0.13), residues: 1264 sheet: 0.81 (0.79), residues: 48 loop : -0.46 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 154 HIS 0.003 0.001 HIS B 337 PHE 0.010 0.001 PHE A 298 TYR 0.011 0.001 TYR D 415 ARG 0.002 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7642 (mp0) cc_final: 0.7406 (mp0) REVERT: A 420 ILE cc_start: 0.8784 (mm) cc_final: 0.8547 (mt) REVERT: B 33 GLU cc_start: 0.7636 (mp0) cc_final: 0.7401 (mp0) REVERT: B 420 ILE cc_start: 0.8783 (mm) cc_final: 0.8548 (mt) REVERT: C 33 GLU cc_start: 0.7642 (mp0) cc_final: 0.7404 (mp0) REVERT: C 420 ILE cc_start: 0.8784 (mm) cc_final: 0.8544 (mt) REVERT: D 33 GLU cc_start: 0.7637 (mp0) cc_final: 0.7400 (mp0) REVERT: D 420 ILE cc_start: 0.8783 (mm) cc_final: 0.8547 (mt) outliers start: 20 outliers final: 12 residues processed: 192 average time/residue: 2.7035 time to fit residues: 563.6432 Evaluate side-chains 184 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8005 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12328 Z= 0.204 Angle : 0.451 3.828 16728 Z= 0.247 Chirality : 0.035 0.130 2012 Planarity : 0.003 0.029 2040 Dihedral : 4.031 23.111 1760 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.82 % Allowed : 17.02 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.21), residues: 1508 helix: 2.82 (0.14), residues: 1264 sheet: 0.58 (0.79), residues: 48 loop : -0.51 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 328 HIS 0.004 0.001 HIS C 337 PHE 0.013 0.002 PHE B 125 TYR 0.008 0.001 TYR C 182 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.841 Fit side-chains REVERT: A 33 GLU cc_start: 0.7653 (mp0) cc_final: 0.7365 (mp0) REVERT: A 354 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8189 (mm-30) REVERT: A 420 ILE cc_start: 0.8777 (mm) cc_final: 0.8569 (mt) REVERT: B 33 GLU cc_start: 0.7647 (mp0) cc_final: 0.7359 (mp0) REVERT: B 354 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8193 (mm-30) REVERT: B 420 ILE cc_start: 0.8782 (mm) cc_final: 0.8575 (mt) REVERT: C 33 GLU cc_start: 0.7650 (mp0) cc_final: 0.7357 (mp0) REVERT: C 354 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8194 (mm-30) REVERT: C 420 ILE cc_start: 0.8780 (mm) cc_final: 0.8569 (mt) REVERT: D 33 GLU cc_start: 0.7649 (mp0) cc_final: 0.7359 (mp0) REVERT: D 354 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8189 (mm-30) REVERT: D 420 ILE cc_start: 0.8783 (mm) cc_final: 0.8574 (mt) outliers start: 24 outliers final: 12 residues processed: 188 average time/residue: 2.6413 time to fit residues: 541.7165 Evaluate side-chains 176 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.8019 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12328 Z= 0.259 Angle : 0.472 4.373 16728 Z= 0.259 Chirality : 0.036 0.129 2012 Planarity : 0.004 0.056 2040 Dihedral : 4.140 23.566 1760 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.82 % Allowed : 17.93 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.21), residues: 1508 helix: 2.71 (0.14), residues: 1264 sheet: 0.54 (0.80), residues: 48 loop : -0.58 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 328 HIS 0.004 0.001 HIS D 337 PHE 0.012 0.002 PHE A 298 TYR 0.009 0.001 TYR D 182 ARG 0.005 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 2.159 Fit side-chains REVERT: A 33 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7320 (mp0) REVERT: A 354 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8204 (mm-30) REVERT: A 420 ILE cc_start: 0.8790 (mm) cc_final: 0.8575 (mt) REVERT: A 423 GLN cc_start: 0.6130 (mm110) cc_final: 0.5231 (pt0) REVERT: B 33 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7313 (mp0) REVERT: B 354 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8209 (mm-30) REVERT: B 420 ILE cc_start: 0.8791 (mm) cc_final: 0.8576 (mt) REVERT: B 423 GLN cc_start: 0.6118 (mm110) cc_final: 0.5221 (pt0) REVERT: C 33 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7312 (mp0) REVERT: C 354 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 420 ILE cc_start: 0.8789 (mm) cc_final: 0.8573 (mt) REVERT: C 423 GLN cc_start: 0.6128 (mm110) cc_final: 0.5226 (pt0) REVERT: D 33 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7317 (mp0) REVERT: D 354 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 420 ILE cc_start: 0.8790 (mm) cc_final: 0.8575 (mt) REVERT: D 423 GLN cc_start: 0.6130 (mm110) cc_final: 0.5235 (pt0) outliers start: 24 outliers final: 8 residues processed: 192 average time/residue: 2.6179 time to fit residues: 549.3370 Evaluate side-chains 180 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12328 Z= 0.191 Angle : 0.445 4.086 16728 Z= 0.243 Chirality : 0.034 0.129 2012 Planarity : 0.003 0.032 2040 Dihedral : 3.820 20.093 1756 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 18.16 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.21), residues: 1508 helix: 2.83 (0.14), residues: 1264 sheet: 0.46 (0.81), residues: 48 loop : -0.50 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 328 HIS 0.004 0.001 HIS A 337 PHE 0.017 0.002 PHE A 125 TYR 0.006 0.001 TYR D 182 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.787 Fit side-chains REVERT: A 120 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7138 (t160) REVERT: A 354 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 420 ILE cc_start: 0.8799 (mm) cc_final: 0.8581 (mt) REVERT: A 423 GLN cc_start: 0.6148 (mm110) cc_final: 0.5244 (pt0) REVERT: B 120 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7130 (t160) REVERT: B 354 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8089 (mm-30) REVERT: B 420 ILE cc_start: 0.8818 (mm) cc_final: 0.8595 (mt) REVERT: B 423 GLN cc_start: 0.6111 (mm110) cc_final: 0.5206 (pt0) REVERT: C 120 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7129 (t160) REVERT: C 354 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8089 (mm-30) REVERT: C 420 ILE cc_start: 0.8816 (mm) cc_final: 0.8592 (mt) REVERT: C 423 GLN cc_start: 0.6121 (mm110) cc_final: 0.5208 (pt0) REVERT: D 120 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7154 (t160) REVERT: D 354 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8082 (mm-30) REVERT: D 420 ILE cc_start: 0.8817 (mm) cc_final: 0.8596 (mt) REVERT: D 423 GLN cc_start: 0.6124 (mm110) cc_final: 0.5219 (pt0) outliers start: 24 outliers final: 12 residues processed: 186 average time/residue: 2.6565 time to fit residues: 539.5279 Evaluate side-chains 177 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12328 Z= 0.202 Angle : 0.447 4.396 16728 Z= 0.245 Chirality : 0.034 0.129 2012 Planarity : 0.004 0.034 2040 Dihedral : 3.768 18.928 1756 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 17.93 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.21), residues: 1508 helix: 2.83 (0.14), residues: 1264 sheet: 0.41 (0.81), residues: 48 loop : -0.49 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 328 HIS 0.004 0.001 HIS C 337 PHE 0.010 0.001 PHE D 11 TYR 0.007 0.001 TYR D 182 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.984 Fit side-chains REVERT: A 354 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 423 GLN cc_start: 0.6166 (mm110) cc_final: 0.5213 (pt0) REVERT: B 354 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 420 ILE cc_start: 0.8806 (mm) cc_final: 0.8599 (mt) REVERT: B 423 GLN cc_start: 0.6141 (mm110) cc_final: 0.5206 (pt0) REVERT: C 354 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8090 (mm-30) REVERT: C 420 ILE cc_start: 0.8804 (mm) cc_final: 0.8598 (mt) REVERT: C 423 GLN cc_start: 0.6150 (mm110) cc_final: 0.5209 (pt0) REVERT: D 354 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8083 (mm-30) REVERT: D 420 ILE cc_start: 0.8806 (mm) cc_final: 0.8601 (mt) REVERT: D 423 GLN cc_start: 0.6151 (mm110) cc_final: 0.5218 (pt0) outliers start: 24 outliers final: 12 residues processed: 188 average time/residue: 2.7974 time to fit residues: 571.3039 Evaluate side-chains 179 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12328 Z= 0.263 Angle : 0.474 4.453 16728 Z= 0.261 Chirality : 0.036 0.128 2012 Planarity : 0.004 0.039 2040 Dihedral : 3.905 21.531 1756 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.82 % Allowed : 17.86 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.21), residues: 1508 helix: 2.69 (0.14), residues: 1264 sheet: 0.43 (0.80), residues: 48 loop : -0.55 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.004 0.001 HIS A 337 PHE 0.020 0.002 PHE B 125 TYR 0.009 0.001 TYR A 182 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.732 Fit side-chains REVERT: A 354 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8218 (mm-30) REVERT: A 423 GLN cc_start: 0.6114 (mm110) cc_final: 0.5153 (pt0) REVERT: B 354 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 420 ILE cc_start: 0.8805 (mm) cc_final: 0.8587 (mt) REVERT: B 423 GLN cc_start: 0.6089 (mm110) cc_final: 0.5145 (pt0) REVERT: C 354 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8224 (mm-30) REVERT: C 420 ILE cc_start: 0.8801 (mm) cc_final: 0.8583 (mt) REVERT: C 423 GLN cc_start: 0.6098 (mm110) cc_final: 0.5149 (pt0) REVERT: D 354 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8211 (mm-30) REVERT: D 420 ILE cc_start: 0.8802 (mm) cc_final: 0.8587 (mt) REVERT: D 423 GLN cc_start: 0.6099 (mm110) cc_final: 0.5155 (pt0) outliers start: 24 outliers final: 12 residues processed: 202 average time/residue: 2.6556 time to fit residues: 583.6425 Evaluate side-chains 191 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12328 Z= 0.148 Angle : 0.432 5.044 16728 Z= 0.236 Chirality : 0.034 0.129 2012 Planarity : 0.003 0.030 2040 Dihedral : 3.666 16.285 1756 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.22 % Allowed : 18.77 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.21), residues: 1508 helix: 2.95 (0.14), residues: 1264 sheet: 0.34 (0.82), residues: 48 loop : -0.44 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.004 0.001 HIS C 337 PHE 0.010 0.001 PHE C 11 TYR 0.005 0.001 TYR B 182 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.6683 (ttm-80) cc_final: 0.6468 (ttm-80) REVERT: A 354 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 420 ILE cc_start: 0.8800 (mm) cc_final: 0.8557 (mt) REVERT: A 423 GLN cc_start: 0.6058 (mm110) cc_final: 0.5125 (pt0) REVERT: B 31 ARG cc_start: 0.6677 (ttm-80) cc_final: 0.6461 (ttm-80) REVERT: B 354 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 423 GLN cc_start: 0.6059 (mm110) cc_final: 0.5146 (pt0) REVERT: C 31 ARG cc_start: 0.6671 (ttm-80) cc_final: 0.6453 (ttm-80) REVERT: C 354 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8066 (mm-30) REVERT: C 423 GLN cc_start: 0.6100 (mm110) cc_final: 0.5164 (pt0) REVERT: D 31 ARG cc_start: 0.6677 (ttm-80) cc_final: 0.6462 (ttm-80) REVERT: D 354 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8168 (mm-30) REVERT: D 423 GLN cc_start: 0.6101 (mm110) cc_final: 0.5172 (pt0) outliers start: 16 outliers final: 12 residues processed: 176 average time/residue: 2.8872 time to fit residues: 550.4477 Evaluate side-chains 169 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.3980 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12328 Z= 0.174 Angle : 0.434 4.365 16728 Z= 0.238 Chirality : 0.034 0.129 2012 Planarity : 0.003 0.027 2040 Dihedral : 3.574 14.359 1756 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.91 % Allowed : 19.83 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.21), residues: 1508 helix: 2.95 (0.14), residues: 1264 sheet: 0.40 (0.83), residues: 48 loop : -0.44 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.004 0.001 HIS D 337 PHE 0.009 0.001 PHE B 11 TYR 0.006 0.001 TYR B 182 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.6683 (ttm-80) cc_final: 0.6461 (ttm-80) REVERT: A 354 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8192 (mm-30) REVERT: A 420 ILE cc_start: 0.8785 (mm) cc_final: 0.8578 (mt) REVERT: A 423 GLN cc_start: 0.6156 (mm110) cc_final: 0.5165 (pt0) REVERT: B 31 ARG cc_start: 0.6676 (ttm-80) cc_final: 0.6452 (ttm-80) REVERT: B 354 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8195 (mm-30) REVERT: B 423 GLN cc_start: 0.6129 (mm110) cc_final: 0.5133 (pt0) REVERT: C 31 ARG cc_start: 0.6671 (ttm-80) cc_final: 0.6446 (ttm-80) REVERT: C 354 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8194 (mm-30) REVERT: C 423 GLN cc_start: 0.6176 (mm110) cc_final: 0.5184 (pt0) REVERT: D 31 ARG cc_start: 0.6679 (ttm-80) cc_final: 0.6456 (ttm-80) REVERT: D 354 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8190 (mm-30) REVERT: D 423 GLN cc_start: 0.6139 (mm110) cc_final: 0.5143 (pt0) outliers start: 12 outliers final: 12 residues processed: 173 average time/residue: 3.0063 time to fit residues: 567.0172 Evaluate side-chains 173 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7963 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12328 Z= 0.137 Angle : 0.416 4.366 16728 Z= 0.227 Chirality : 0.033 0.131 2012 Planarity : 0.003 0.024 2040 Dihedral : 3.447 11.116 1756 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.61 % Allowed : 19.98 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.21), residues: 1508 helix: 3.08 (0.14), residues: 1264 sheet: 0.40 (0.84), residues: 48 loop : -0.43 (0.52), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.003 0.001 HIS D 337 PHE 0.021 0.001 PHE D 125 TYR 0.004 0.001 TYR B 182 ARG 0.003 0.000 ARG C 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.6656 (ttm-80) cc_final: 0.6440 (ttm-80) REVERT: A 354 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 423 GLN cc_start: 0.6135 (mm110) cc_final: 0.5141 (pt0) REVERT: B 31 ARG cc_start: 0.6649 (ttm-80) cc_final: 0.6433 (ttm-80) REVERT: B 354 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8182 (mm-30) REVERT: B 423 GLN cc_start: 0.6129 (mm110) cc_final: 0.5147 (pt0) REVERT: C 31 ARG cc_start: 0.6644 (ttm-80) cc_final: 0.6426 (ttm-80) REVERT: C 354 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8181 (mm-30) REVERT: C 423 GLN cc_start: 0.6140 (mm110) cc_final: 0.5149 (pt0) REVERT: D 31 ARG cc_start: 0.6651 (ttm-80) cc_final: 0.6436 (ttm-80) REVERT: D 354 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8179 (mm-30) REVERT: D 423 GLN cc_start: 0.6140 (mm110) cc_final: 0.5158 (pt0) outliers start: 8 outliers final: 8 residues processed: 177 average time/residue: 3.0653 time to fit residues: 587.0501 Evaluate side-chains 168 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.141811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103287 restraints weight = 35812.045| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.68 r_work: 0.2950 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12328 Z= 0.134 Angle : 0.417 4.017 16728 Z= 0.227 Chirality : 0.033 0.128 2012 Planarity : 0.003 0.024 2040 Dihedral : 3.362 10.478 1756 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.30 % Allowed : 20.36 % Favored : 79.33 % 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: 4.00 (0.21), residues: 1508 helix: 3.14 (0.13), residues: 1264 sheet: 0.32 (0.83), residues: 48 loop : -0.39 (0.52), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.003 0.001 HIS B 337 PHE 0.009 0.001 PHE A 11 TYR 0.004 0.001 TYR B 182 ARG 0.003 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9226.12 seconds wall clock time: 160 minutes 17.76 seconds (9617.76 seconds total)