Starting phenix.real_space_refine on Wed Mar 5 20:57:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws6_32748/03_2025/7ws6_32748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws6_32748/03_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_32748/03_2025/7ws6_32748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws6_32748/03_2025/7ws6_32748.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws6_32748/03_2025/7ws6_32748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws6_32748/03_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-5624/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: 5.33, per 1000 atoms: 1.51 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: 0.83 Conformation dependent library (CDL) restraints added in 449.2 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: 0.93 Time building geometry restraints manager: 1.02 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: 0.010 Normalize map: mean=0, sd=1: 11.740 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.110 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- 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 : 0.370 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: 0.1909 time to fit residues: 24.1000 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 : 0.371 ------------------------------------------------------------------------------- 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 = 0.108267 restraints weight = 9391.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.112989 restraints weight = 7025.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.115239 restraints weight = 3785.878| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.7693 (p90) cc_final: 0.7421 (p90) REVERT: I 31 ASP cc_start: 0.8538 (p0) cc_final: 0.8111 (p0) REVERT: I 59 ASP cc_start: 0.8146 (t0) cc_final: 0.7886 (t0) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.1655 time to fit residues: 20.3594 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 : 0.372 ------------------------------------------------------------------------------- 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: 0.7980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 overall best weight: 0.5012 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.124739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.109353 restraints weight = 9151.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.114584 restraints weight = 6572.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.116355 restraints weight = 3380.994| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3622 Z= 0.211 Angle : 0.656 9.328 4922 Z= 0.332 Chirality : 0.046 0.199 529 Planarity : 0.004 0.032 638 Dihedral : 4.789 17.312 499 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.84 % Allowed : 16.02 % Favored : 81.14 % 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: -3.66 (0.64), residues: 24 sheet: 0.30 (0.45), residues: 132 loop : -1.05 (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 0.011 0.001 PHE C 486 TYR 0.020 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 108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8371 (p0) cc_final: 0.8034 (t70) REVERT: C 340 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8289 (tm-30) REVERT: H 27 GLN cc_start: 0.8340 (mp10) cc_final: 0.7997 (mp10) REVERT: H 49 TYR cc_start: 0.7583 (p90) cc_final: 0.7319 (p90) REVERT: I 31 ASP cc_start: 0.8529 (p0) cc_final: 0.8125 (p0) REVERT: I 59 ASP cc_start: 0.8153 (t0) cc_final: 0.7733 (t0) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.1677 time to fit residues: 20.5961 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.0030 chunk 11 optimal weight: 0.0010 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.126674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.111646 restraints weight = 9506.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.116309 restraints weight = 7035.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118063 restraints weight = 3862.158| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2943 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= 0.179 Angle : 0.643 9.883 4922 Z= 0.320 Chirality : 0.045 0.174 529 Planarity : 0.004 0.032 638 Dihedral : 4.481 15.165 499 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.58 % Allowed : 19.90 % 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: -1.11 (0.37), residues: 445 helix: -3.71 (0.61), residues: 24 sheet: 0.29 (0.45), residues: 132 loop : -0.99 (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 0.009 0.000 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 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8299 (p0) cc_final: 0.7889 (t0) REVERT: C 340 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8201 (tm-30) REVERT: H 27 GLN cc_start: 0.8368 (mp10) cc_final: 0.8123 (mp10) REVERT: I 31 ASP cc_start: 0.8442 (p0) cc_final: 0.8042 (p0) REVERT: I 59 ASP cc_start: 0.8084 (t0) cc_final: 0.7604 (t0) REVERT: I 60 TYR cc_start: 0.8397 (m-10) cc_final: 0.8137 (m-10) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.1643 time to fit residues: 19.2418 Evaluate side-chains 91 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3883 r_free = 0.3883 target = 0.119458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103887 restraints weight = 9711.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109199 restraints weight = 7086.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110746 restraints weight = 3702.182| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 3622 Z= 0.419 Angle : 0.732 8.022 4922 Z= 0.383 Chirality : 0.048 0.197 529 Planarity : 0.004 0.034 638 Dihedral : 5.562 20.877 499 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.88 % Allowed : 20.67 % Favored : 75.45 % 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: -1.40 (0.37), residues: 445 helix: -2.98 (0.85), residues: 18 sheet: -0.12 (0.43), residues: 141 loop : -1.25 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 436 HIS 0.004 0.002 HIS I 35 PHE 0.026 0.002 PHE C 486 TYR 0.021 0.002 TYR I 102 ARG 0.003 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 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 31 ASP cc_start: 0.8648 (p0) cc_final: 0.8203 (p0) REVERT: I 46 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7935 (mm-30) REVERT: I 59 ASP cc_start: 0.8135 (t0) cc_final: 0.7718 (t0) REVERT: I 60 TYR cc_start: 0.8446 (m-10) cc_final: 0.8219 (m-10) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 0.1830 time to fit residues: 21.2158 Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 472 ILE 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 Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 0.2980 chunk 1 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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** ** 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 = 0.3951 r_free = 0.3951 target = 0.124136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.108555 restraints weight = 9666.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113118 restraints weight = 6887.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.114865 restraints weight = 3787.146| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3398 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= 0.202 Angle : 0.658 7.595 4922 Z= 0.337 Chirality : 0.045 0.172 529 Planarity : 0.004 0.033 638 Dihedral : 4.919 19.067 499 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.88 % Allowed : 21.71 % 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: -1.12 (0.37), residues: 445 helix: -2.76 (0.89), residues: 18 sheet: 0.25 (0.45), residues: 132 loop : -1.12 (0.33), residues: 295 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 I 29 TYR 0.022 0.001 TYR I 102 ARG 0.006 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: 15 poor density : 87 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8335 (p0) cc_final: 0.7891 (t0) REVERT: C 340 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8277 (tm-30) REVERT: H 27 GLN cc_start: 0.8402 (mp10) cc_final: 0.8173 (mp10) REVERT: I 31 ASP cc_start: 0.8512 (p0) cc_final: 0.8109 (p0) REVERT: I 59 ASP cc_start: 0.8042 (t0) cc_final: 0.7594 (t0) REVERT: I 60 TYR cc_start: 0.8489 (m-10) cc_final: 0.8184 (m-10) REVERT: I 68 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.7127 (m-10) REVERT: I 111 ASP cc_start: 0.9133 (t0) cc_final: 0.8894 (t0) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.2002 time to fit residues: 23.5068 Evaluate side-chains 91 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 494 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 68 PHE 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: 1.9990 chunk 1 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3925 r_free = 0.3925 target = 0.122313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106659 restraints weight = 9494.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111810 restraints weight = 6761.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.112941 restraints weight = 3679.701| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3622 Z= 0.266 Angle : 0.695 7.694 4922 Z= 0.358 Chirality : 0.046 0.174 529 Planarity : 0.004 0.034 638 Dihedral : 5.168 21.979 499 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.88 % Allowed : 22.74 % Favored : 73.39 % 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: -1.30 (0.37), residues: 445 helix: -2.73 (0.90), residues: 18 sheet: -0.05 (0.44), residues: 141 loop : -1.20 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.002 HIS I 35 PHE 0.016 0.002 PHE C 456 TYR 0.024 0.002 TYR C 473 ARG 0.007 0.001 ARG H 24 *********************** 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 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: C 406 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6249 (mt-10) REVERT: C 460 ASN cc_start: 0.8722 (m-40) cc_final: 0.8464 (m-40) REVERT: H 71 PHE cc_start: 0.6637 (m-80) cc_final: 0.6319 (m-80) REVERT: I 31 ASP cc_start: 0.8547 (p0) cc_final: 0.8151 (p0) REVERT: I 46 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7823 (mm-30) REVERT: I 59 ASP cc_start: 0.8064 (t0) cc_final: 0.7662 (t0) REVERT: I 60 TYR cc_start: 0.8608 (m-10) cc_final: 0.8214 (m-10) REVERT: I 100 ARG cc_start: 0.9044 (ptm160) cc_final: 0.8836 (ptm160) REVERT: I 111 ASP cc_start: 0.9122 (t0) cc_final: 0.8821 (t0) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.1914 time to fit residues: 21.3102 Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain C residue 430 THR 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 75 ILE 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: 0.0040 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 0.3250 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109933 restraints weight = 9515.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114940 restraints weight = 6892.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116181 restraints weight = 3670.218| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3741 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= 0.199 Angle : 0.686 7.794 4922 Z= 0.347 Chirality : 0.045 0.164 529 Planarity : 0.004 0.031 638 Dihedral : 4.714 20.560 499 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.10 % Allowed : 23.00 % 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: -1.16 (0.37), residues: 445 helix: -2.66 (0.89), residues: 18 sheet: 0.26 (0.46), residues: 132 loop : -1.19 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.026 0.001 PHE I 68 TYR 0.019 0.001 TYR I 102 ARG 0.008 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 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: H 27 GLN cc_start: 0.8465 (mp10) cc_final: 0.8087 (mp10) REVERT: I 31 ASP cc_start: 0.8478 (p0) cc_final: 0.8079 (p0) REVERT: I 46 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7867 (mm-30) REVERT: I 59 ASP cc_start: 0.7994 (t0) cc_final: 0.7584 (t0) REVERT: I 60 TYR cc_start: 0.8584 (m-10) cc_final: 0.8168 (m-10) REVERT: I 111 ASP cc_start: 0.9057 (t0) cc_final: 0.8779 (t0) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 0.1733 time to fit residues: 19.9475 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 21 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.124188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.110074 restraints weight = 9476.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113094 restraints weight = 6233.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.114053 restraints weight = 4519.072| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3849 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= 0.236 Angle : 0.711 8.166 4922 Z= 0.362 Chirality : 0.046 0.173 529 Planarity : 0.004 0.038 638 Dihedral : 4.827 20.614 499 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.36 % Allowed : 23.51 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.37), residues: 445 helix: -2.57 (0.92), residues: 18 sheet: 0.20 (0.45), residues: 132 loop : -1.26 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.051 0.002 PHE I 68 TYR 0.019 0.001 TYR I 102 ARG 0.008 0.001 ARG H 24 *********************** 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 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: C 338 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8125 (t80) REVERT: C 460 ASN cc_start: 0.8641 (m-40) cc_final: 0.8341 (m-40) REVERT: I 31 ASP cc_start: 0.8510 (p0) cc_final: 0.8094 (p0) REVERT: I 46 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7883 (mm-30) REVERT: I 59 ASP cc_start: 0.8068 (t0) cc_final: 0.7645 (t0) REVERT: I 60 TYR cc_start: 0.8620 (m-10) cc_final: 0.8199 (m-10) REVERT: I 111 ASP cc_start: 0.9043 (t0) cc_final: 0.8737 (t0) outliers start: 13 outliers final: 12 residues processed: 93 average time/residue: 0.1780 time to fit residues: 20.5406 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.0000 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 414 GLN H 34 ASN H 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.124644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109193 restraints weight = 9568.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114048 restraints weight = 6765.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.115613 restraints weight = 3685.074| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3906 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= 0.233 Angle : 0.721 8.612 4922 Z= 0.365 Chirality : 0.046 0.175 529 Planarity : 0.004 0.038 638 Dihedral : 4.769 20.066 499 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.84 % Allowed : 24.55 % Favored : 72.61 % 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: -1.30 (0.37), residues: 445 helix: -2.52 (0.94), residues: 18 sheet: 0.20 (0.46), residues: 129 loop : -1.31 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.042 0.002 PHE I 68 TYR 0.019 0.001 TYR I 102 ARG 0.009 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 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: C 338 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8137 (t80) REVERT: C 339 ASP cc_start: 0.8177 (p0) cc_final: 0.7876 (m-30) REVERT: C 340 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 460 ASN cc_start: 0.8669 (m-40) cc_final: 0.8395 (m-40) REVERT: H 4 MET cc_start: 0.8124 (pmm) cc_final: 0.7732 (pmm) REVERT: I 31 ASP cc_start: 0.8493 (p0) cc_final: 0.8075 (p0) REVERT: I 46 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7968 (mm-30) REVERT: I 59 ASP cc_start: 0.8091 (t0) cc_final: 0.7649 (t0) REVERT: I 60 TYR cc_start: 0.8621 (m-10) cc_final: 0.8231 (m-10) REVERT: I 111 ASP cc_start: 0.9047 (t0) cc_final: 0.8734 (t0) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.1675 time to fit residues: 18.6209 Evaluate side-chains 92 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 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 = 0.3964 r_free = 0.3964 target = 0.124781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109393 restraints weight = 9532.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.114171 restraints weight = 6723.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.116159 restraints weight = 3620.370| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 3622 Z= 0.371 Angle : 1.366 59.193 4922 Z= 0.781 Chirality : 0.051 0.501 529 Planarity : 0.004 0.036 638 Dihedral : 4.775 20.050 499 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.58 % Allowed : 24.55 % Favored : 72.87 % 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: -1.30 (0.37), residues: 445 helix: -2.52 (0.94), residues: 18 sheet: 0.20 (0.45), residues: 129 loop : -1.32 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.042 0.002 PHE I 68 TYR 0.018 0.001 TYR I 102 ARG 0.007 0.000 ARG H 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.96 seconds wall clock time: 35 minutes 25.57 seconds (2125.57 seconds total)