Starting phenix.real_space_refine on Tue Feb 11 01:51:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws6_32748/02_2025/7ws6_32748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws6_32748/02_2025/7ws6_32748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws6_32748/02_2025/7ws6_32748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws6_32748/02_2025/7ws6_32748.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws6_32748/02_2025/7ws6_32748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws6_32748/02_2025/7ws6_32748.cif" } resolution = 3.8 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= -0.002 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2245 2.51 5 N 597 2.21 5 O 674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3531 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1747 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 203} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Time building chain proxies: 5.75, per 1000 atoms: 1.63 Number of scatterers: 3531 At special positions: 0 Unit cell: (59.072, 94.016, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 674 8.00 N 597 7.00 C 2245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 414.5 milliseconds 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 8.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.527A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.539A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.512A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.554A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.542A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.771A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.604A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.866A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.680A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.952A pdb=" N ASP I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS I 98 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.952A pdb=" N ASP I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1132 1.34 - 1.46: 899 1.46 - 1.58: 1573 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3622 Sorted by residual: bond pdb=" N ASP I 31 " pdb=" CA ASP I 31 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.22e-02 6.72e+03 8.47e+00 bond pdb=" N ASP C 442 " pdb=" CA ASP C 442 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.52e+00 bond pdb=" N ARG C 346 " pdb=" CA ARG C 346 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.12e+00 bond pdb=" N LYS C 440 " pdb=" CA LYS C 440 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.32e-02 5.74e+03 5.37e+00 bond pdb=" N ARG C 493 " pdb=" CA ARG C 493 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.19e-02 7.06e+03 5.36e+00 ... (remaining 3617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4597 1.21 - 2.42: 249 2.42 - 3.64: 61 3.64 - 4.85: 11 4.85 - 6.06: 4 Bond angle restraints: 4922 Sorted by residual: angle pdb=" CA TYR H 32 " pdb=" C TYR H 32 " pdb=" O TYR H 32 " ideal model delta sigma weight residual 122.13 118.09 4.04 1.13e+00 7.83e-01 1.28e+01 angle pdb=" C SER C 438 " pdb=" N ASN C 439 " pdb=" CA ASN C 439 " ideal model delta sigma weight residual 121.14 115.95 5.19 1.75e+00 3.27e-01 8.80e+00 angle pdb=" CA ARG C 493 " pdb=" C ARG C 493 " pdb=" O ARG C 493 " ideal model delta sigma weight residual 121.16 118.08 3.08 1.13e+00 7.83e-01 7.43e+00 angle pdb=" CA ARG C 346 " pdb=" C ARG C 346 " pdb=" O ARG C 346 " ideal model delta sigma weight residual 120.66 117.69 2.97 1.15e+00 7.56e-01 6.65e+00 angle pdb=" CA LYS H 45 " pdb=" C LYS H 45 " pdb=" O LYS H 45 " ideal model delta sigma weight residual 121.44 118.43 3.01 1.17e+00 7.31e-01 6.62e+00 ... (remaining 4917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1952 17.96 - 35.91: 163 35.91 - 53.87: 24 53.87 - 71.82: 6 71.82 - 89.78: 3 Dihedral angle restraints: 2148 sinusoidal: 836 harmonic: 1312 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 35.32 57.68 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CA PRO C 337 " pdb=" C PRO C 337 " pdb=" N PHE C 338 " pdb=" CA PHE C 338 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 63.07 29.93 1 1.00e+01 1.00e-02 1.28e+01 ... (remaining 2145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 375 0.041 - 0.082: 106 0.082 - 0.124: 43 0.124 - 0.165: 3 0.165 - 0.206: 2 Chirality restraints: 529 Sorted by residual: chirality pdb=" CB ILE H 75 " pdb=" CA ILE H 75 " pdb=" CG1 ILE H 75 " pdb=" CG2 ILE H 75 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR H 94 " pdb=" N THR H 94 " pdb=" C THR H 94 " pdb=" CB THR H 94 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ARG C 346 " pdb=" N ARG C 346 " pdb=" C ARG C 346 " pdb=" CB ARG C 346 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 526 not shown) Planarity restraints: 638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 24 " -0.143 9.50e-02 1.11e+02 6.45e-02 3.09e+00 pdb=" NE ARG H 24 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 24 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 24 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 24 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 106 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO I 107 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 107 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 60 " -0.006 2.00e-02 2.50e+03 8.32e-03 1.39e+00 pdb=" CG TYR I 60 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR I 60 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR I 60 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR I 60 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR I 60 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 60 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 60 " 0.000 2.00e-02 2.50e+03 ... (remaining 635 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1013 2.81 - 3.33: 3100 3.33 - 3.85: 5601 3.85 - 4.38: 6356 4.38 - 4.90: 10946 Nonbonded interactions: 27016 Sorted by model distance: nonbonded pdb=" OD1 ASP C 339 " pdb=" N GLU C 340 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP I 62 " pdb=" N SER I 63 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASN H 34 " pdb=" OG SER I 109 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASP I 99 " pdb=" N ARG I 100 " model vdw 2.322 3.120 ... (remaining 27011 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 0.036 3622 Z= 0.224 Angle : 0.682 6.060 4922 Z= 0.391 Chirality : 0.046 0.206 529 Planarity : 0.004 0.065 638 Dihedral : 13.454 89.776 1297 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.37 (0.36), residues: 445 helix: -3.69 (0.62), residues: 26 sheet: 0.38 (0.45), residues: 133 loop : -1.33 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 113 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.001 PHE C 486 TYR 0.020 0.001 TYR I 60 ARG 0.013 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: H 34 ASN cc_start: 0.8518 (m110) cc_final: 0.7462 (m110) REVERT: H 97 TYR cc_start: 0.8609 (m-80) cc_final: 0.8334 (m-80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2002 time to fit residues: 25.2248 Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.123756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.108251 restraints weight = 9391.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113127 restraints weight = 7015.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115057 restraints weight = 3752.417| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3622 Z= 0.272 Angle : 0.664 7.964 4922 Z= 0.344 Chirality : 0.047 0.153 529 Planarity : 0.004 0.033 638 Dihedral : 5.079 18.372 499 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.33 % Allowed : 13.18 % Favored : 84.50 % 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: -1.21 (0.37), residues: 445 helix: -3.70 (0.60), residues: 24 sheet: 0.24 (0.44), residues: 141 loop : -1.12 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 36 HIS 0.002 0.001 HIS I 35 PHE 0.020 0.002 PHE C 486 TYR 0.018 0.002 TYR I 102 ARG 0.005 0.001 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.7693 (p90) cc_final: 0.7420 (p90) REVERT: I 31 ASP cc_start: 0.8539 (p0) cc_final: 0.8112 (p0) REVERT: I 59 ASP cc_start: 0.8146 (t0) cc_final: 0.7888 (t0) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.1686 time to fit residues: 20.6232 Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.0000 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.124562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109322 restraints weight = 9200.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.114363 restraints weight = 6632.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116011 restraints weight = 3528.932| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3622 Z= 0.225 Angle : 0.656 9.310 4922 Z= 0.334 Chirality : 0.046 0.199 529 Planarity : 0.004 0.033 638 Dihedral : 4.861 17.913 499 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.84 % Allowed : 16.54 % 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: -1.18 (0.37), residues: 445 helix: -3.64 (0.65), residues: 24 sheet: 0.28 (0.46), residues: 132 loop : -1.07 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.013 0.001 PHE C 486 TYR 0.019 0.001 TYR I 102 ARG 0.006 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8403 (p0) cc_final: 0.8059 (t70) REVERT: H 49 TYR cc_start: 0.7632 (p90) cc_final: 0.7362 (p90) REVERT: I 31 ASP cc_start: 0.8526 (p0) cc_final: 0.8136 (p0) REVERT: I 59 ASP cc_start: 0.8147 (t0) cc_final: 0.7737 (t0) outliers start: 11 outliers final: 7 residues processed: 100 average time/residue: 0.1813 time to fit residues: 21.6890 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 0.0870 chunk 5 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.125825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.110645 restraints weight = 9512.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.115969 restraints weight = 6954.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.117227 restraints weight = 3506.172| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3622 Z= 0.189 Angle : 0.650 9.780 4922 Z= 0.324 Chirality : 0.045 0.178 529 Planarity : 0.004 0.032 638 Dihedral : 4.609 15.879 499 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 20.16 % Favored : 77.52 % 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: -1.15 (0.37), residues: 445 helix: -3.67 (0.63), residues: 24 sheet: 0.29 (0.45), residues: 132 loop : -1.04 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 53 HIS 0.003 0.001 HIS I 35 PHE 0.010 0.001 PHE H 62 TYR 0.019 0.001 TYR I 102 ARG 0.008 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8382 (p0) cc_final: 0.7798 (t0) REVERT: C 340 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 516 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6913 (mt-10) REVERT: I 31 ASP cc_start: 0.8504 (p0) cc_final: 0.8097 (p0) REVERT: I 59 ASP cc_start: 0.8132 (t0) cc_final: 0.7641 (t0) REVERT: I 60 TYR cc_start: 0.8446 (m-10) cc_final: 0.8186 (m-10) outliers start: 9 outliers final: 8 residues processed: 102 average time/residue: 0.1659 time to fit residues: 20.7940 Evaluate side-chains 92 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.122476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107263 restraints weight = 9659.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112377 restraints weight = 6956.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114065 restraints weight = 3669.541| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3622 Z= 0.260 Angle : 0.663 8.200 4922 Z= 0.339 Chirality : 0.046 0.181 529 Planarity : 0.004 0.032 638 Dihedral : 4.916 18.103 499 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.36 % Allowed : 20.67 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.37), residues: 445 helix: -3.07 (0.81), residues: 18 sheet: 0.02 (0.43), residues: 141 loop : -1.12 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.016 0.002 PHE C 486 TYR 0.020 0.001 TYR I 102 ARG 0.005 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8448 (p0) cc_final: 0.8062 (t70) REVERT: C 340 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8244 (tm-30) REVERT: I 31 ASP cc_start: 0.8569 (p0) cc_final: 0.8150 (p0) REVERT: I 59 ASP cc_start: 0.8145 (t0) cc_final: 0.7675 (t0) REVERT: I 60 TYR cc_start: 0.8453 (m-10) cc_final: 0.8229 (m-10) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.1719 time to fit residues: 20.1703 Evaluate side-chains 91 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108207 restraints weight = 9608.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.113235 restraints weight = 6938.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114178 restraints weight = 3807.380| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3622 Z= 0.237 Angle : 0.676 9.852 4922 Z= 0.342 Chirality : 0.045 0.175 529 Planarity : 0.004 0.041 638 Dihedral : 4.884 19.067 499 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.62 % Allowed : 21.96 % Favored : 74.42 % 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: -1.23 (0.37), residues: 445 helix: -2.87 (0.84), residues: 18 sheet: 0.12 (0.43), residues: 139 loop : -1.21 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.002 HIS I 35 PHE 0.012 0.001 PHE C 486 TYR 0.020 0.002 TYR I 102 ARG 0.009 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8401 (p0) cc_final: 0.7920 (t0) REVERT: C 340 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8275 (tm-30) REVERT: I 31 ASP cc_start: 0.8490 (p0) cc_final: 0.8079 (p0) REVERT: I 46 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7711 (mm-30) REVERT: I 59 ASP cc_start: 0.8059 (t0) cc_final: 0.7628 (t0) REVERT: I 60 TYR cc_start: 0.8478 (m-10) cc_final: 0.8217 (m-10) REVERT: I 83 MET cc_start: 0.8464 (mmm) cc_final: 0.8199 (mmm) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.1673 time to fit residues: 19.4501 Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.0030 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.123699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107813 restraints weight = 9553.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112708 restraints weight = 6877.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.115182 restraints weight = 3629.450| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3622 Z= 0.225 Angle : 0.676 9.096 4922 Z= 0.342 Chirality : 0.046 0.171 529 Planarity : 0.004 0.033 638 Dihedral : 4.885 21.816 499 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.88 % Allowed : 23.77 % Favored : 72.35 % 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: -1.27 (0.37), residues: 445 helix: -2.95 (0.83), residues: 18 sheet: 0.11 (0.44), residues: 139 loop : -1.24 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.011 0.001 PHE C 456 TYR 0.021 0.001 TYR C 473 ARG 0.002 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8372 (p0) cc_final: 0.7910 (t0) REVERT: C 340 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 460 ASN cc_start: 0.8654 (m-40) cc_final: 0.8391 (m-40) REVERT: H 71 PHE cc_start: 0.6577 (m-80) cc_final: 0.6325 (m-80) REVERT: H 82 ASP cc_start: 0.7236 (m-30) cc_final: 0.6988 (m-30) REVERT: I 31 ASP cc_start: 0.8491 (p0) cc_final: 0.8091 (p0) REVERT: I 46 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7834 (mm-30) REVERT: I 59 ASP cc_start: 0.7982 (t0) cc_final: 0.7596 (t0) REVERT: I 60 TYR cc_start: 0.8539 (m-10) cc_final: 0.8138 (m-10) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.1719 time to fit residues: 20.2640 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.124396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108896 restraints weight = 9544.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.113721 restraints weight = 6932.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.115216 restraints weight = 3684.286| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3622 Z= 0.221 Angle : 0.687 8.653 4922 Z= 0.347 Chirality : 0.045 0.168 529 Planarity : 0.004 0.051 638 Dihedral : 4.842 21.029 499 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.13 % Allowed : 21.96 % Favored : 73.90 % 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: -1.32 (0.37), residues: 445 helix: -3.01 (0.83), residues: 18 sheet: 0.12 (0.43), residues: 139 loop : -1.29 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.010 0.001 PHE I 29 TYR 0.019 0.001 TYR I 102 ARG 0.014 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8417 (p0) cc_final: 0.7932 (t0) REVERT: C 340 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 460 ASN cc_start: 0.8677 (m-40) cc_final: 0.8386 (m-40) REVERT: H 37 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: I 46 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7890 (mm-30) REVERT: I 59 ASP cc_start: 0.8058 (t0) cc_final: 0.7648 (t0) REVERT: I 60 TYR cc_start: 0.8430 (m-10) cc_final: 0.8116 (m-10) outliers start: 16 outliers final: 15 residues processed: 96 average time/residue: 0.1699 time to fit residues: 19.8861 Evaluate side-chains 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.123350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.107860 restraints weight = 9486.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112976 restraints weight = 6870.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.113832 restraints weight = 3605.425| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3622 Z= 0.253 Angle : 0.721 9.532 4922 Z= 0.365 Chirality : 0.046 0.176 529 Planarity : 0.004 0.033 638 Dihedral : 4.979 20.877 499 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.62 % Allowed : 23.51 % Favored : 72.87 % 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: -1.47 (0.36), residues: 445 helix: -2.99 (0.84), residues: 18 sheet: -0.06 (0.43), residues: 141 loop : -1.38 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.019 0.002 PHE H 71 TYR 0.019 0.001 TYR I 102 ARG 0.002 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8411 (p0) cc_final: 0.7941 (t0) REVERT: C 340 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 460 ASN cc_start: 0.8714 (m-40) cc_final: 0.8434 (m-40) REVERT: H 37 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: I 46 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7888 (mm-30) REVERT: I 59 ASP cc_start: 0.7953 (t0) cc_final: 0.7582 (t0) REVERT: I 60 TYR cc_start: 0.8481 (m-10) cc_final: 0.8133 (m-10) outliers start: 14 outliers final: 13 residues processed: 92 average time/residue: 0.1687 time to fit residues: 18.8587 Evaluate side-chains 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 34 ASN H 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.125582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.110682 restraints weight = 9673.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.114390 restraints weight = 6656.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.116211 restraints weight = 4150.533| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3622 Z= 0.211 Angle : 0.717 10.026 4922 Z= 0.359 Chirality : 0.045 0.171 529 Planarity : 0.005 0.059 638 Dihedral : 4.673 19.585 499 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.58 % Allowed : 24.55 % Favored : 72.87 % 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: -1.36 (0.36), residues: 445 helix: -3.05 (0.81), residues: 18 sheet: 0.22 (0.45), residues: 132 loop : -1.37 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.019 0.001 PHE H 71 TYR 0.019 0.001 TYR I 102 ARG 0.017 0.001 ARG H 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: H 37 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: I 46 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7836 (mm-30) REVERT: I 59 ASP cc_start: 0.8029 (t0) cc_final: 0.7603 (t0) REVERT: I 60 TYR cc_start: 0.8553 (m-10) cc_final: 0.8181 (m-10) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.1549 time to fit residues: 17.0683 Evaluate side-chains 90 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 0.0870 chunk 41 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 35 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.125636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110363 restraints weight = 9596.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.115407 restraints weight = 6862.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.116361 restraints weight = 3599.321| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 3622 Z= 0.392 Angle : 1.368 59.199 4922 Z= 0.781 Chirality : 0.052 0.580 529 Planarity : 0.004 0.049 638 Dihedral : 4.661 19.403 499 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.33 % Allowed : 23.77 % Favored : 73.90 % Cbeta Deviations : 0.24 % 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: -1.37 (0.36), residues: 445 helix: -3.05 (0.81), residues: 18 sheet: 0.21 (0.44), residues: 132 loop : -1.37 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.018 0.002 PHE I 68 TYR 0.019 0.001 TYR I 102 ARG 0.010 0.001 ARG C 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.57 seconds wall clock time: 34 minutes 20.20 seconds (2060.20 seconds total)