Starting phenix.real_space_refine on Tue Mar 3 11:49:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws6_32748/03_2026/7ws6_32748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws6_32748/03_2026/7ws6_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_2026/7ws6_32748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws6_32748/03_2026/7ws6_32748.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws6_32748/03_2026/7ws6_32748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws6_32748/03_2026/7ws6_32748.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.85, per 1000 atoms: 0.24 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: 0.25 Conformation dependent library (CDL) restraints added in 134.5 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: 0.13 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: 0.44 Time building geometry restraints manager: 0.35 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: 12.680 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- 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 3627 Z= 0.198 Angle : 0.685 6.060 4932 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.001 ARG H 24 TYR 0.020 0.001 TYR I 60 PHE 0.016 0.001 PHE C 486 TRP 0.006 0.001 TRP I 113 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3622) covalent geometry : angle 0.68236 ( 4922) SS BOND : bond 0.00429 ( 5) SS BOND : angle 1.38584 ( 10) hydrogen bonds : bond 0.27965 ( 90) hydrogen bonds : angle 10.33063 ( 240) *********************** 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 : 0.089 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: 0.8333 (m-80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0821 time to fit residues: 10.3028 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 : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3354 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.127880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.112724 restraints weight = 9624.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117406 restraints weight = 7291.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.119590 restraints weight = 3764.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.120101 restraints weight = 3070.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120387 restraints weight = 2620.995| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3627 Z= 0.123 Angle : 0.633 7.745 4932 Z= 0.321 Chirality : 0.046 0.161 529 Planarity : 0.004 0.032 638 Dihedral : 4.620 17.135 499 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.33 % Allowed : 10.85 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.37), residues: 445 helix: -3.81 (0.56), residues: 24 sheet: 0.57 (0.46), residues: 130 loop : -1.09 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 61 TYR 0.018 0.002 TYR I 102 PHE 0.014 0.001 PHE I 68 TRP 0.007 0.001 TRP I 36 HIS 0.002 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3622) covalent geometry : angle 0.63238 ( 4922) SS BOND : bond 0.00249 ( 5) SS BOND : angle 1.01931 ( 10) hydrogen bonds : bond 0.04376 ( 90) hydrogen bonds : angle 6.73824 ( 240) *********************** 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 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8356 (p0) cc_final: 0.7889 (t0) REVERT: C 340 GLU cc_start: 0.8636 (pp20) cc_final: 0.8193 (tm-30) REVERT: H 27 GLN cc_start: 0.8414 (mp10) cc_final: 0.8010 (mp10) REVERT: H 49 TYR cc_start: 0.7434 (p90) cc_final: 0.7200 (p90) REVERT: I 31 ASP cc_start: 0.8370 (p0) cc_final: 0.7979 (p0) REVERT: I 59 ASP cc_start: 0.8005 (t0) cc_final: 0.7783 (t0) outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 0.0644 time to fit residues: 8.0287 Evaluate side-chains 93 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** 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 = 0.3959 r_free = 0.3959 target = 0.124298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109098 restraints weight = 9235.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.114336 restraints weight = 6872.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.116311 restraints weight = 3365.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117125 restraints weight = 2738.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.117676 restraints weight = 2276.311| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3627 Z= 0.175 Angle : 0.664 7.351 4932 Z= 0.343 Chirality : 0.046 0.187 529 Planarity : 0.004 0.032 638 Dihedral : 4.875 16.968 499 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.36 % Allowed : 18.60 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.37), residues: 445 helix: -3.71 (0.61), residues: 24 sheet: 0.23 (0.44), residues: 132 loop : -1.00 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 24 TYR 0.020 0.002 TYR I 102 PHE 0.017 0.002 PHE C 486 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3622) covalent geometry : angle 0.65584 ( 4922) SS BOND : bond 0.00765 ( 5) SS BOND : angle 2.33363 ( 10) hydrogen bonds : bond 0.04037 ( 90) hydrogen bonds : angle 6.06146 ( 240) *********************** 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 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8390 (p0) cc_final: 0.7947 (t0) REVERT: C 340 GLU cc_start: 0.8600 (pp20) cc_final: 0.8204 (tm-30) REVERT: H 49 TYR cc_start: 0.7666 (p90) cc_final: 0.7394 (p90) REVERT: H 81 GLU cc_start: 0.7817 (pp20) cc_final: 0.7502 (pp20) REVERT: I 31 ASP cc_start: 0.8485 (p0) cc_final: 0.8066 (p0) REVERT: I 59 ASP cc_start: 0.8051 (t0) cc_final: 0.7657 (t0) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.0735 time to fit residues: 8.6707 Evaluate side-chains 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 401 VAL 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 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 6 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.121811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106521 restraints weight = 9355.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.112325 restraints weight = 6923.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.113974 restraints weight = 3356.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.114535 restraints weight = 2694.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.115031 restraints weight = 2183.364| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3627 Z= 0.224 Angle : 0.689 7.359 4932 Z= 0.361 Chirality : 0.047 0.197 529 Planarity : 0.004 0.032 638 Dihedral : 5.311 19.011 499 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.36 % Allowed : 21.71 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.37), residues: 445 helix: -3.07 (0.81), residues: 18 sheet: -0.03 (0.43), residues: 141 loop : -1.01 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 24 TYR 0.020 0.002 TYR I 102 PHE 0.022 0.002 PHE C 486 TRP 0.012 0.002 TRP C 436 HIS 0.003 0.002 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 3622) covalent geometry : angle 0.68105 ( 4922) SS BOND : bond 0.00478 ( 5) SS BOND : angle 2.44409 ( 10) hydrogen bonds : bond 0.03915 ( 90) hydrogen bonds : angle 6.11990 ( 240) *********************** 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 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.7739 (p90) cc_final: 0.7504 (p90) REVERT: H 81 GLU cc_start: 0.7704 (pp20) cc_final: 0.7319 (pp20) REVERT: I 31 ASP cc_start: 0.8572 (p0) cc_final: 0.8191 (p0) REVERT: I 46 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7992 (mm-30) REVERT: I 59 ASP cc_start: 0.8093 (t0) cc_final: 0.7642 (t0) REVERT: I 60 TYR cc_start: 0.8454 (m-10) cc_final: 0.8231 (m-10) REVERT: I 111 ASP cc_start: 0.9160 (t0) cc_final: 0.8956 (t0) outliers start: 13 outliers final: 10 residues processed: 101 average time/residue: 0.0660 time to fit residues: 8.0576 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 401 VAL 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 I residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.123060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.107658 restraints weight = 9344.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.112852 restraints weight = 6913.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114408 restraints weight = 3584.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.115119 restraints weight = 2776.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116180 restraints weight = 2287.601| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3627 Z= 0.168 Angle : 0.687 7.719 4932 Z= 0.350 Chirality : 0.046 0.178 529 Planarity : 0.004 0.032 638 Dihedral : 5.105 19.818 499 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.13 % Allowed : 22.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.37), residues: 445 helix: -3.08 (0.81), residues: 18 sheet: 0.10 (0.45), residues: 132 loop : -1.06 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 24 TYR 0.019 0.002 TYR I 102 PHE 0.014 0.002 PHE H 62 TRP 0.013 0.001 TRP I 53 HIS 0.003 0.002 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3622) covalent geometry : angle 0.67969 ( 4922) SS BOND : bond 0.00533 ( 5) SS BOND : angle 2.25068 ( 10) hydrogen bonds : bond 0.03634 ( 90) hydrogen bonds : angle 5.99548 ( 240) *********************** 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 109 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8278 (p0) cc_final: 0.7947 (t0) REVERT: C 340 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8279 (tm-30) REVERT: I 31 ASP cc_start: 0.8533 (p0) cc_final: 0.8128 (p0) REVERT: I 59 ASP cc_start: 0.8090 (t0) cc_final: 0.7635 (t0) REVERT: I 60 TYR cc_start: 0.8442 (m-10) cc_final: 0.8224 (m-10) REVERT: I 111 ASP cc_start: 0.9198 (t0) cc_final: 0.8904 (t0) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.0786 time to fit residues: 9.5230 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 : 0.087 ------------------------------------------------------------------------------- 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 401 VAL 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 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: 1.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.107480 restraints weight = 9398.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112412 restraints weight = 6928.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.113849 restraints weight = 3669.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.114496 restraints weight = 2884.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.115400 restraints weight = 2438.543| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3627 Z= 0.170 Angle : 0.685 7.658 4932 Z= 0.351 Chirality : 0.046 0.178 529 Planarity : 0.004 0.034 638 Dihedral : 5.185 24.637 499 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.13 % Allowed : 23.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.37), residues: 445 helix: -3.06 (0.83), residues: 18 sheet: -0.09 (0.43), residues: 141 loop : -1.08 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 24 TYR 0.022 0.002 TYR C 473 PHE 0.014 0.002 PHE C 486 TRP 0.009 0.001 TRP I 53 HIS 0.004 0.002 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 3622) covalent geometry : angle 0.67772 ( 4922) SS BOND : bond 0.00519 ( 5) SS BOND : angle 2.25835 ( 10) hydrogen bonds : bond 0.03565 ( 90) hydrogen bonds : angle 5.93079 ( 240) *********************** 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 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: C 339 ASP cc_start: 0.8294 (p0) cc_final: 0.7973 (t70) REVERT: C 340 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8290 (tm-30) REVERT: I 31 ASP cc_start: 0.8523 (p0) cc_final: 0.8151 (p0) REVERT: I 46 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7926 (mm-30) REVERT: I 59 ASP cc_start: 0.8050 (t0) cc_final: 0.7615 (t0) REVERT: I 60 TYR cc_start: 0.8483 (m-10) cc_final: 0.8248 (m-10) REVERT: I 83 MET cc_start: 0.8538 (mmm) cc_final: 0.8279 (mmm) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.0614 time to fit residues: 7.2357 Evaluate side-chains 93 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 401 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR 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 I residue 5 VAL Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.125267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109896 restraints weight = 9728.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115387 restraints weight = 6806.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.116533 restraints weight = 3440.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.117170 restraints weight = 2801.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.117671 restraints weight = 2374.876| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3627 Z= 0.127 Angle : 0.678 7.233 4932 Z= 0.344 Chirality : 0.046 0.205 529 Planarity : 0.004 0.032 638 Dihedral : 4.813 23.917 499 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.13 % Allowed : 23.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.37), residues: 445 helix: -3.14 (0.81), residues: 18 sheet: 0.12 (0.45), residues: 132 loop : -1.04 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 24 TYR 0.018 0.001 TYR I 102 PHE 0.013 0.001 PHE C 490 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3622) covalent geometry : angle 0.67123 ( 4922) SS BOND : bond 0.00456 ( 5) SS BOND : angle 2.16367 ( 10) hydrogen bonds : bond 0.03364 ( 90) hydrogen bonds : angle 5.80821 ( 240) *********************** 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 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: H 27 GLN cc_start: 0.8403 (mp10) cc_final: 0.8173 (mp10) REVERT: H 71 PHE cc_start: 0.6499 (m-80) cc_final: 0.6271 (m-80) REVERT: I 31 ASP cc_start: 0.8462 (p0) cc_final: 0.8096 (p0) REVERT: I 59 ASP cc_start: 0.7948 (t0) cc_final: 0.7532 (t0) REVERT: I 60 TYR cc_start: 0.8545 (m-10) cc_final: 0.8247 (m-10) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.0672 time to fit residues: 8.3455 Evaluate side-chains 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 401 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 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 = 0.3929 r_free = 0.3929 target = 0.123002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.107298 restraints weight = 9697.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.112246 restraints weight = 6957.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113473 restraints weight = 3812.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114170 restraints weight = 3000.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115218 restraints weight = 2513.906| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3627 Z= 0.189 Angle : 0.727 8.221 4932 Z= 0.377 Chirality : 0.047 0.195 529 Planarity : 0.005 0.035 638 Dihedral : 5.182 31.976 499 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.17 % Allowed : 23.51 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.37), residues: 445 helix: -3.04 (0.84), residues: 18 sheet: 0.08 (0.45), residues: 132 loop : -1.19 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 24 TYR 0.019 0.002 TYR I 102 PHE 0.017 0.002 PHE I 68 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3622) covalent geometry : angle 0.72094 ( 4922) SS BOND : bond 0.00517 ( 5) SS BOND : angle 2.20838 ( 10) hydrogen bonds : bond 0.03496 ( 90) hydrogen bonds : angle 5.84923 ( 240) *********************** 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 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: C 460 ASN cc_start: 0.8774 (m-40) cc_final: 0.8537 (m-40) REVERT: H 71 PHE cc_start: 0.6640 (m-80) cc_final: 0.6408 (m-80) REVERT: H 79 GLN cc_start: 0.8611 (pp30) cc_final: 0.8240 (pp30) REVERT: I 31 ASP cc_start: 0.8523 (p0) cc_final: 0.8112 (p0) REVERT: I 59 ASP cc_start: 0.7999 (t0) cc_final: 0.7591 (t0) REVERT: I 60 TYR cc_start: 0.8468 (m-10) cc_final: 0.8175 (m-10) outliers start: 20 outliers final: 17 residues processed: 95 average time/residue: 0.0610 time to fit residues: 7.0984 Evaluate side-chains 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 401 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 46 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 I residue 5 VAL Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.123742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108115 restraints weight = 9346.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113185 restraints weight = 6737.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.113859 restraints weight = 3680.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114057 restraints weight = 3153.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115339 restraints weight = 2842.845| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3627 Z= 0.159 Angle : 0.733 7.494 4932 Z= 0.377 Chirality : 0.047 0.210 529 Planarity : 0.004 0.039 638 Dihedral : 5.097 31.565 499 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.88 % Allowed : 24.29 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.37), residues: 445 helix: -3.03 (0.85), residues: 18 sheet: 0.14 (0.45), residues: 132 loop : -1.23 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 24 TYR 0.019 0.001 TYR I 102 PHE 0.026 0.002 PHE I 68 TRP 0.007 0.001 TRP I 53 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3622) covalent geometry : angle 0.72746 ( 4922) SS BOND : bond 0.00497 ( 5) SS BOND : angle 2.15953 ( 10) hydrogen bonds : bond 0.03450 ( 90) hydrogen bonds : angle 5.85538 ( 240) *********************** 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 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: C 460 ASN cc_start: 0.8739 (m-40) cc_final: 0.8515 (m-40) REVERT: H 79 GLN cc_start: 0.8555 (pp30) cc_final: 0.8206 (pp30) REVERT: I 31 ASP cc_start: 0.8454 (p0) cc_final: 0.8049 (p0) REVERT: I 59 ASP cc_start: 0.7946 (t0) cc_final: 0.7577 (t0) REVERT: I 60 TYR cc_start: 0.8502 (m-10) cc_final: 0.8166 (m-10) outliers start: 15 outliers final: 15 residues processed: 95 average time/residue: 0.0679 time to fit residues: 7.8632 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 401 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR 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 I residue 5 VAL Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 414 GLN H 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.124519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.109265 restraints weight = 9688.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113087 restraints weight = 6482.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115019 restraints weight = 4111.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115585 restraints weight = 3014.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.116201 restraints weight = 2512.114| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3627 Z= 0.149 Angle : 0.761 10.311 4932 Z= 0.382 Chirality : 0.047 0.207 529 Planarity : 0.005 0.040 638 Dihedral : 5.013 31.593 499 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.13 % Allowed : 24.81 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.36), residues: 445 helix: -3.03 (0.85), residues: 18 sheet: 0.00 (0.44), residues: 134 loop : -1.23 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 24 TYR 0.019 0.001 TYR I 102 PHE 0.019 0.002 PHE I 68 TRP 0.007 0.001 TRP I 53 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3622) covalent geometry : angle 0.75527 ( 4922) SS BOND : bond 0.00484 ( 5) SS BOND : angle 2.13736 ( 10) hydrogen bonds : bond 0.03411 ( 90) hydrogen bonds : angle 5.81442 ( 240) ********************** 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 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: C 338 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8075 (t80) REVERT: C 460 ASN cc_start: 0.8724 (m-40) cc_final: 0.8454 (m-40) REVERT: H 49 TYR cc_start: 0.7777 (p90) cc_final: 0.7431 (p90) REVERT: H 79 GLN cc_start: 0.8543 (pp30) cc_final: 0.8214 (pp30) REVERT: I 31 ASP cc_start: 0.8476 (p0) cc_final: 0.8076 (p0) REVERT: I 59 ASP cc_start: 0.7972 (t0) cc_final: 0.7554 (t0) REVERT: I 60 TYR cc_start: 0.8578 (m-10) cc_final: 0.8239 (m-10) outliers start: 16 outliers final: 14 residues processed: 97 average time/residue: 0.0687 time to fit residues: 8.1745 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 401 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR 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 I residue 5 VAL Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107006 restraints weight = 9372.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111895 restraints weight = 6762.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113193 restraints weight = 3683.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113856 restraints weight = 2929.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114815 restraints weight = 2435.788| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3627 Z= 0.197 Angle : 0.789 12.594 4932 Z= 0.399 Chirality : 0.048 0.213 529 Planarity : 0.005 0.040 638 Dihedral : 5.249 31.672 499 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.13 % Allowed : 24.81 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.36), residues: 445 helix: -2.93 (0.89), residues: 18 sheet: -0.20 (0.43), residues: 138 loop : -1.33 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 24 TYR 0.019 0.002 TYR I 102 PHE 0.045 0.002 PHE I 68 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.002 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 3622) covalent geometry : angle 0.78366 ( 4922) SS BOND : bond 0.00530 ( 5) SS BOND : angle 2.26723 ( 10) hydrogen bonds : bond 0.03612 ( 90) hydrogen bonds : angle 5.89599 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 999.20 seconds wall clock time: 17 minutes 53.35 seconds (1073.35 seconds total)