Starting phenix.real_space_refine on Fri May 23 14:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jma_36411/05_2025/8jma_36411_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jma_36411/05_2025/8jma_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/cci-nas-00/data/ceres_data/8jma_36411/05_2025/8jma_36411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jma_36411/05_2025/8jma_36411.map" model { file = "/net/cci-nas-00/data/ceres_data/8jma_36411/05_2025/8jma_36411_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jma_36411/05_2025/8jma_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-5687/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: 15.04, per 1000 atoms: 0.61 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: 6.83 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: 1.92 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: 9.18 Time building geometry restraints manager: 8.07 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.710 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: 0.410 Extract box with map and model: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.480 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.370 ------------------------------------------------------------------------------- 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= 0.219 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 Details of bonding type rmsd hydrogen bonds : bond 0.09802 ( 1072) hydrogen bonds : angle 4.78280 ( 3204) covalent geometry : bond 0.00443 (12328) covalent geometry : angle 0.51192 (16728) *********************** 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 to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.767 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: 2.5839 time to fit residues: 474.1799 Evaluate side-chains 168 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.098956 restraints weight = 35755.838| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.67 r_work: 0.2890 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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= 0.172 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 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1072) hydrogen bonds : angle 4.14962 ( 3204) covalent geometry : bond 0.00355 (12328) covalent geometry : angle 0.46494 (16728) *********************** 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 to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7863 (mp0) cc_final: 0.7593 (mp0) REVERT: A 420 ILE cc_start: 0.8758 (mm) cc_final: 0.8504 (mt) REVERT: B 33 GLU cc_start: 0.7854 (mp0) cc_final: 0.7580 (mp0) REVERT: B 420 ILE cc_start: 0.8750 (mm) cc_final: 0.8493 (mt) REVERT: C 33 GLU cc_start: 0.7859 (mp0) cc_final: 0.7587 (mp0) REVERT: C 420 ILE cc_start: 0.8750 (mm) cc_final: 0.8491 (mt) REVERT: D 33 GLU cc_start: 0.7846 (mp0) cc_final: 0.7576 (mp0) REVERT: D 420 ILE cc_start: 0.8753 (mm) cc_final: 0.8497 (mt) outliers start: 20 outliers final: 12 residues processed: 192 average time/residue: 2.7994 time to fit residues: 583.5391 Evaluate side-chains 184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 118 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.137666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097990 restraints weight = 35598.876| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.69 r_work: 0.2885 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12328 Z= 0.178 Angle : 0.465 4.262 16728 Z= 0.255 Chirality : 0.035 0.130 2012 Planarity : 0.003 0.034 2040 Dihedral : 4.109 23.075 1760 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.07 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: 3.45 (0.21), residues: 1508 helix: 2.74 (0.14), residues: 1264 sheet: 0.57 (0.79), residues: 48 loop : -0.55 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 328 HIS 0.004 0.001 HIS D 337 PHE 0.014 0.002 PHE C 125 TYR 0.009 0.001 TYR C 182 ARG 0.002 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 1072) hydrogen bonds : angle 4.13353 ( 3204) covalent geometry : bond 0.00372 (12328) covalent geometry : angle 0.46523 (16728) *********************** 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 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.810 Fit side-chains REVERT: A 33 GLU cc_start: 0.7864 (mp0) cc_final: 0.7543 (mp0) REVERT: A 354 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8317 (mm-30) REVERT: A 420 ILE cc_start: 0.8780 (mm) cc_final: 0.8547 (mt) REVERT: B 33 GLU cc_start: 0.7851 (mp0) cc_final: 0.7529 (mp0) REVERT: B 354 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 420 ILE cc_start: 0.8775 (mm) cc_final: 0.8540 (mt) REVERT: C 33 GLU cc_start: 0.7846 (mp0) cc_final: 0.7524 (mp0) REVERT: C 354 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8316 (mm-30) REVERT: C 420 ILE cc_start: 0.8769 (mm) cc_final: 0.8530 (mt) REVERT: D 33 GLU cc_start: 0.7840 (mp0) cc_final: 0.7519 (mp0) REVERT: D 354 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8329 (mm-30) REVERT: D 420 ILE cc_start: 0.8769 (mm) cc_final: 0.8534 (mt) outliers start: 24 outliers final: 12 residues processed: 188 average time/residue: 2.3881 time to fit residues: 494.6161 Evaluate side-chains 180 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 5 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.137866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098190 restraints weight = 35937.022| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.70 r_work: 0.2892 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12328 Z= 0.167 Angle : 0.457 4.059 16728 Z= 0.251 Chirality : 0.035 0.130 2012 Planarity : 0.003 0.033 2040 Dihedral : 4.046 22.510 1760 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 18.24 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.21), residues: 1508 helix: 2.77 (0.14), residues: 1264 sheet: 0.52 (0.80), residues: 48 loop : -0.56 (0.49), 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 0.016 0.002 PHE D 125 TYR 0.008 0.001 TYR D 182 ARG 0.003 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 1072) hydrogen bonds : angle 4.09467 ( 3204) covalent geometry : bond 0.00346 (12328) covalent geometry : angle 0.45733 (16728) *********************** 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 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.774 Fit side-chains REVERT: A 354 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 420 ILE cc_start: 0.8814 (mm) cc_final: 0.8573 (mt) REVERT: A 423 GLN cc_start: 0.5932 (mm110) cc_final: 0.4936 (pt0) REVERT: B 354 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8323 (mm-30) REVERT: B 420 ILE cc_start: 0.8806 (mm) cc_final: 0.8550 (mt) REVERT: B 423 GLN cc_start: 0.5908 (mm110) cc_final: 0.4924 (pt0) REVERT: C 354 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8318 (mm-30) REVERT: C 420 ILE cc_start: 0.8803 (mm) cc_final: 0.8545 (mt) REVERT: C 423 GLN cc_start: 0.5916 (mm110) cc_final: 0.4923 (pt0) REVERT: D 354 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8320 (mm-30) REVERT: D 420 ILE cc_start: 0.8804 (mm) cc_final: 0.8548 (mt) REVERT: D 423 GLN cc_start: 0.5926 (mm110) cc_final: 0.4924 (pt0) outliers start: 24 outliers final: 8 residues processed: 184 average time/residue: 2.7573 time to fit residues: 551.1848 Evaluate side-chains 172 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 118 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.137463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097968 restraints weight = 35988.525| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.69 r_work: 0.2886 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12328 Z= 0.178 Angle : 0.464 4.267 16728 Z= 0.255 Chirality : 0.035 0.129 2012 Planarity : 0.003 0.036 2040 Dihedral : 3.919 22.194 1756 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.60 % Allowed : 17.86 % Favored : 80.55 % 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: 3.39 (0.21), residues: 1508 helix: 2.71 (0.14), residues: 1264 sheet: 0.47 (0.79), residues: 48 loop : -0.60 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.004 0.001 HIS B 337 PHE 0.011 0.002 PHE A 298 TYR 0.009 0.001 TYR D 182 ARG 0.002 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 1072) hydrogen bonds : angle 4.12029 ( 3204) covalent geometry : bond 0.00374 (12328) covalent geometry : angle 0.46409 (16728) *********************** 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 198 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.922 Fit side-chains REVERT: A 354 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 420 ILE cc_start: 0.8800 (mm) cc_final: 0.8558 (mt) REVERT: A 423 GLN cc_start: 0.5996 (mm110) cc_final: 0.4950 (pt0) REVERT: B 354 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 420 ILE cc_start: 0.8809 (mm) cc_final: 0.8557 (mt) REVERT: B 423 GLN cc_start: 0.5971 (mm110) cc_final: 0.4936 (pt0) REVERT: C 354 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8202 (mm-30) REVERT: C 420 ILE cc_start: 0.8803 (mm) cc_final: 0.8552 (mt) REVERT: C 423 GLN cc_start: 0.5980 (mm110) cc_final: 0.4933 (pt0) REVERT: D 354 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8331 (mm-30) REVERT: D 420 ILE cc_start: 0.8804 (mm) cc_final: 0.8557 (mt) REVERT: D 423 GLN cc_start: 0.5986 (mm110) cc_final: 0.4932 (pt0) outliers start: 21 outliers final: 12 residues processed: 190 average time/residue: 2.5309 time to fit residues: 526.7679 Evaluate side-chains 186 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 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 120 ASN B 120 ASN C 120 ASN D 120 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.098276 restraints weight = 35811.486| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.69 r_work: 0.2895 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12328 Z= 0.166 Angle : 0.460 4.356 16728 Z= 0.252 Chirality : 0.035 0.129 2012 Planarity : 0.003 0.032 2040 Dihedral : 3.867 21.148 1756 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.44 % Allowed : 17.93 % Favored : 80.62 % 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: 3.45 (0.21), residues: 1508 helix: 2.75 (0.14), residues: 1264 sheet: 0.37 (0.80), residues: 48 loop : -0.58 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.004 0.001 HIS B 337 PHE 0.011 0.001 PHE A 11 TYR 0.008 0.001 TYR A 182 ARG 0.002 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 1072) hydrogen bonds : angle 4.10237 ( 3204) covalent geometry : bond 0.00345 (12328) covalent geometry : angle 0.45959 (16728) *********************** 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 183 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.785 Fit side-chains REVERT: A 354 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8191 (mm-30) REVERT: A 420 ILE cc_start: 0.8794 (mm) cc_final: 0.8569 (mt) REVERT: A 423 GLN cc_start: 0.6003 (mm110) cc_final: 0.4920 (pt0) REVERT: B 354 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8202 (mm-30) REVERT: B 420 ILE cc_start: 0.8798 (mm) cc_final: 0.8561 (mt) REVERT: B 423 GLN cc_start: 0.5975 (mm110) cc_final: 0.4906 (pt0) REVERT: C 354 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8198 (mm-30) REVERT: C 420 ILE cc_start: 0.8791 (mm) cc_final: 0.8556 (mt) REVERT: C 423 GLN cc_start: 0.5985 (mm110) cc_final: 0.4903 (pt0) REVERT: D 354 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 420 ILE cc_start: 0.8795 (mm) cc_final: 0.8562 (mt) REVERT: D 423 GLN cc_start: 0.5997 (mm110) cc_final: 0.4910 (pt0) outliers start: 19 outliers final: 12 residues processed: 183 average time/residue: 2.8220 time to fit residues: 559.8161 Evaluate side-chains 179 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 87 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.137307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097826 restraints weight = 35873.626| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.69 r_work: 0.2891 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12328 Z= 0.177 Angle : 0.466 4.516 16728 Z= 0.255 Chirality : 0.035 0.128 2012 Planarity : 0.003 0.036 2040 Dihedral : 3.893 21.607 1756 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 17.63 % Favored : 80.85 % 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: 3.39 (0.21), residues: 1508 helix: 2.71 (0.14), residues: 1264 sheet: 0.41 (0.80), residues: 48 loop : -0.60 (0.50), 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 0.019 0.002 PHE B 125 TYR 0.008 0.001 TYR C 182 ARG 0.002 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 1072) hydrogen bonds : angle 4.12100 ( 3204) covalent geometry : bond 0.00373 (12328) covalent geometry : angle 0.46580 (16728) *********************** 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 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.951 Fit side-chains REVERT: A 354 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 420 ILE cc_start: 0.8786 (mm) cc_final: 0.8558 (mt) REVERT: A 423 GLN cc_start: 0.5945 (mm110) cc_final: 0.4892 (pt0) REVERT: B 354 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8328 (mm-30) REVERT: B 420 ILE cc_start: 0.8791 (mm) cc_final: 0.8552 (mt) REVERT: B 423 GLN cc_start: 0.5919 (mm110) cc_final: 0.4878 (pt0) REVERT: C 354 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8327 (mm-30) REVERT: C 420 ILE cc_start: 0.8783 (mm) cc_final: 0.8545 (mt) REVERT: C 423 GLN cc_start: 0.5929 (mm110) cc_final: 0.4878 (pt0) REVERT: D 354 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8333 (mm-30) REVERT: D 420 ILE cc_start: 0.8787 (mm) cc_final: 0.8553 (mt) REVERT: D 423 GLN cc_start: 0.5941 (mm110) cc_final: 0.4882 (pt0) outliers start: 20 outliers final: 12 residues processed: 188 average time/residue: 2.8039 time to fit residues: 575.1807 Evaluate side-chains 176 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 137 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.136857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.097314 restraints weight = 35882.011| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.69 r_work: 0.2879 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12328 Z= 0.205 Angle : 0.488 4.727 16728 Z= 0.267 Chirality : 0.036 0.128 2012 Planarity : 0.004 0.042 2040 Dihedral : 4.052 24.862 1756 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.52 % Allowed : 17.33 % 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: 3.24 (0.21), residues: 1508 helix: 2.60 (0.14), residues: 1264 sheet: 0.45 (0.79), residues: 48 loop : -0.63 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.004 0.001 HIS A 337 PHE 0.022 0.002 PHE A 125 TYR 0.009 0.001 TYR D 182 ARG 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 1072) hydrogen bonds : angle 4.18495 ( 3204) covalent geometry : bond 0.00441 (12328) covalent geometry : angle 0.48836 (16728) *********************** 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 200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 2.062 Fit side-chains REVERT: A 31 ARG cc_start: 0.6361 (ttm-80) cc_final: 0.6093 (ttm-80) REVERT: A 354 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 420 ILE cc_start: 0.8793 (mm) cc_final: 0.8568 (mt) REVERT: A 423 GLN cc_start: 0.6072 (mm110) cc_final: 0.4958 (pt0) REVERT: B 31 ARG cc_start: 0.6339 (ttm-80) cc_final: 0.6072 (ttm-80) REVERT: B 354 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 420 ILE cc_start: 0.8799 (mm) cc_final: 0.8549 (mt) REVERT: B 423 GLN cc_start: 0.6046 (mm110) cc_final: 0.4940 (pt0) REVERT: C 31 ARG cc_start: 0.6331 (ttm-80) cc_final: 0.6063 (ttm-80) REVERT: C 354 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8337 (mm-30) REVERT: C 420 ILE cc_start: 0.8791 (mm) cc_final: 0.8543 (mt) REVERT: C 423 GLN cc_start: 0.6052 (mm110) cc_final: 0.4938 (pt0) REVERT: D 31 ARG cc_start: 0.6347 (ttm-80) cc_final: 0.6079 (ttm-80) REVERT: D 354 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8341 (mm-30) REVERT: D 420 ILE cc_start: 0.8795 (mm) cc_final: 0.8550 (mt) REVERT: D 423 GLN cc_start: 0.6061 (mm110) cc_final: 0.4941 (pt0) outliers start: 20 outliers final: 12 residues processed: 196 average time/residue: 2.7422 time to fit residues: 585.1202 Evaluate side-chains 190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 151 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.137091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.097689 restraints weight = 35947.017| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.69 r_work: 0.2884 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12328 Z= 0.201 Angle : 0.489 5.014 16728 Z= 0.267 Chirality : 0.036 0.128 2012 Planarity : 0.004 0.040 2040 Dihedral : 4.076 25.058 1756 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.91 % Allowed : 17.93 % 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: 3.22 (0.21), residues: 1508 helix: 2.59 (0.14), residues: 1264 sheet: 0.46 (0.80), residues: 48 loop : -0.63 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.004 0.001 HIS A 337 PHE 0.022 0.002 PHE B 125 TYR 0.008 0.001 TYR C 182 ARG 0.005 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 1072) hydrogen bonds : angle 4.18444 ( 3204) covalent geometry : bond 0.00430 (12328) covalent geometry : angle 0.48942 (16728) *********************** 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 191 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.845 Fit side-chains REVERT: A 31 ARG cc_start: 0.6319 (ttm-80) cc_final: 0.6055 (ttm-80) REVERT: A 354 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8325 (mm-30) REVERT: A 420 ILE cc_start: 0.8793 (mm) cc_final: 0.8567 (mt) REVERT: A 423 GLN cc_start: 0.6139 (mm110) cc_final: 0.4980 (pt0) REVERT: B 31 ARG cc_start: 0.6297 (ttm-80) cc_final: 0.6035 (ttm-80) REVERT: B 354 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 420 ILE cc_start: 0.8800 (mm) cc_final: 0.8550 (mt) REVERT: B 423 GLN cc_start: 0.6116 (mm110) cc_final: 0.4966 (pt0) REVERT: C 31 ARG cc_start: 0.6289 (ttm-80) cc_final: 0.6022 (ttm-80) REVERT: C 354 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8331 (mm-30) REVERT: C 420 ILE cc_start: 0.8791 (mm) cc_final: 0.8543 (mt) REVERT: C 423 GLN cc_start: 0.6124 (mm110) cc_final: 0.4968 (pt0) REVERT: D 31 ARG cc_start: 0.6302 (ttm-80) cc_final: 0.6038 (ttm-80) REVERT: D 354 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8336 (mm-30) REVERT: D 420 ILE cc_start: 0.8793 (mm) cc_final: 0.8549 (mt) REVERT: D 423 GLN cc_start: 0.6130 (mm110) cc_final: 0.4965 (pt0) outliers start: 12 outliers final: 12 residues processed: 191 average time/residue: 2.7938 time to fit residues: 580.1417 Evaluate side-chains 191 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 102 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102086 restraints weight = 35825.479| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.68 r_work: 0.2928 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0941 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= 0.114 Angle : 0.438 5.617 16728 Z= 0.237 Chirality : 0.034 0.130 2012 Planarity : 0.004 0.064 2040 Dihedral : 3.739 16.862 1756 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.61 % Allowed : 18.69 % Favored : 80.70 % 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: 3.69 (0.21), residues: 1508 helix: 2.91 (0.14), residues: 1264 sheet: 0.45 (0.83), residues: 48 loop : -0.46 (0.52), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.004 0.001 HIS A 337 PHE 0.011 0.001 PHE D 11 TYR 0.004 0.001 TYR C 96 ARG 0.010 0.001 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1072) hydrogen bonds : angle 3.98554 ( 3204) covalent geometry : bond 0.00219 (12328) covalent geometry : angle 0.43836 (16728) ********************** 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 173 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.6308 (ttm-80) cc_final: 0.6069 (ttm-80) REVERT: A 354 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 423 GLN cc_start: 0.6099 (mm110) cc_final: 0.4966 (pt0) REVERT: B 31 ARG cc_start: 0.6288 (ttm-80) cc_final: 0.6048 (ttm-80) REVERT: B 354 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 423 GLN cc_start: 0.6063 (mm110) cc_final: 0.4930 (pt0) REVERT: C 31 ARG cc_start: 0.6282 (ttm-80) cc_final: 0.6040 (ttm-80) REVERT: C 354 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8170 (mm-30) REVERT: C 423 GLN cc_start: 0.6072 (mm110) cc_final: 0.4940 (pt0) REVERT: D 31 ARG cc_start: 0.6296 (ttm-80) cc_final: 0.6055 (ttm-80) REVERT: D 354 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8174 (mm-30) REVERT: D 423 GLN cc_start: 0.6079 (mm110) cc_final: 0.4936 (pt0) outliers start: 8 outliers final: 8 residues processed: 173 average time/residue: 3.0922 time to fit residues: 576.5405 Evaluate side-chains 165 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 112 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.099156 restraints weight = 35843.770| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.70 r_work: 0.2906 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12328 Z= 0.156 Angle : 0.456 4.749 16728 Z= 0.248 Chirality : 0.035 0.129 2012 Planarity : 0.004 0.099 2040 Dihedral : 3.733 16.862 1756 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.84 % Allowed : 19.15 % 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: 3.59 (0.21), residues: 1508 helix: 2.84 (0.14), residues: 1264 sheet: 0.48 (0.83), residues: 48 loop : -0.51 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 328 HIS 0.004 0.001 HIS D 337 PHE 0.021 0.002 PHE B 125 TYR 0.007 0.001 TYR A 182 ARG 0.012 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1072) hydrogen bonds : angle 4.03770 ( 3204) covalent geometry : bond 0.00322 (12328) covalent geometry : angle 0.45554 (16728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17677.50 seconds wall clock time: 302 minutes 50.33 seconds (18170.33 seconds total)