Starting phenix.real_space_refine on Tue Mar 11 22:53:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8w_33059/03_2025/7x8w_33059_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8w_33059/03_2025/7x8w_33059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2025/7x8w_33059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2025/7x8w_33059.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2025/7x8w_33059_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8w_33059/03_2025/7x8w_33059_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2186 2.51 5 N 574 2.21 5 O 682 1.98 5 H 3214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6674 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3065 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1883 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1627 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.60, per 1000 atoms: 0.69 Number of scatterers: 6674 At special positions: 0 Unit cell: (94.506, 63.004, 99.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 682 8.00 N 574 7.00 C 2186 6.00 H 3214 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN H 59 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.1% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.329A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.694A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.059A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.044A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.906A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.871A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.697A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.697A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 109 hydrogen bonds defined for protein. 258 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: 2.24 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3214 1.04 - 1.23: 82 1.23 - 1.43: 1488 1.43 - 1.62: 1954 1.62 - 1.82: 24 Bond restraints: 6762 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 MAN C 5 " pdb=" C2 MAN C 5 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" N GLN L 1 " pdb=" CA GLN L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N GLN L 1 " pdb=" H GLN L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 6757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 11672 1.32 - 2.64: 358 2.64 - 3.96: 37 3.96 - 5.28: 8 5.28 - 6.60: 5 Bond angle restraints: 12080 Sorted by residual: angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 106.35 6.60 3.00e+00 1.11e-01 4.85e+00 angle pdb=" C3 MAN C 5 " pdb=" C2 MAN C 5 " pdb=" O2 MAN C 5 " ideal model delta sigma weight residual 111.77 105.37 6.40 3.00e+00 1.11e-01 4.55e+00 angle pdb=" C3 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" O2 MAN C 4 " ideal model delta sigma weight residual 111.77 105.65 6.12 3.00e+00 1.11e-01 4.16e+00 angle pdb=" C4 FUC C 6 " pdb=" C3 FUC C 6 " pdb=" O3 FUC C 6 " ideal model delta sigma weight residual 113.24 107.38 5.86 3.00e+00 1.11e-01 3.82e+00 angle pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " pdb=" C5 BMA C 3 " ideal model delta sigma weight residual 118.82 113.51 5.31 3.00e+00 1.11e-01 3.14e+00 ... (remaining 12075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 3140 21.68 - 43.35: 166 43.35 - 65.03: 54 65.03 - 86.71: 16 86.71 - 108.39: 5 Dihedral angle restraints: 3381 sinusoidal: 1856 harmonic: 1525 Sorted by residual: dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.68 108.39 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.69 106.31 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C6 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O4 BMA C 3 " ideal model delta sinusoidal sigma weight residual -163.34 -60.53 -102.81 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 3378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 459 0.055 - 0.110: 68 0.110 - 0.164: 12 0.164 - 0.219: 0 0.219 - 0.273: 2 Chirality restraints: 541 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN H 59 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 538 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 106 " -0.128 9.50e-02 1.11e+02 4.30e-02 2.23e+00 pdb=" NE ARG H 106 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 106 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 106 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG H 106 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 106 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 521 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 400 " -0.004 2.00e-02 2.50e+03 7.44e-03 5.54e-01 pdb=" C PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" O PHE A 400 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL A 401 " -0.004 2.00e-02 2.50e+03 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 616 2.22 - 2.81: 13564 2.81 - 3.41: 16199 3.41 - 4.00: 23473 4.00 - 4.60: 35091 Nonbonded interactions: 88943 Sorted by model distance: nonbonded pdb=" O GLY H 31 " pdb=" H SER H 103 " model vdw 1.624 2.450 nonbonded pdb=" O THR A 345 " pdb="HH22 ARG A 509 " model vdw 1.651 2.450 nonbonded pdb=" OD1 ASN A 360 " pdb=" HG1 THR A 523 " model vdw 1.655 2.450 nonbonded pdb="HH21 ARG A 454 " pdb=" O ASP A 467 " model vdw 1.674 2.450 nonbonded pdb="HH11 ARG A 457 " pdb=" O SER A 459 " model vdw 1.704 2.450 ... (remaining 88938 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.780 Find NCS groups from input model: 0.060 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 0.041 3548 Z= 0.264 Angle : 0.601 6.605 4825 Z= 0.280 Chirality : 0.045 0.273 541 Planarity : 0.004 0.056 611 Dihedral : 16.079 108.387 1376 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -1.35 (0.40), residues: 429 helix: -3.61 (0.73), residues: 27 sheet: 0.25 (0.44), residues: 146 loop : -1.32 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.001 0.001 HIS L 41 PHE 0.009 0.001 PHE A 347 TYR 0.008 0.001 TYR L 51 ARG 0.008 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.4932 time to fit residues: 39.4983 Evaluate side-chains 58 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.069966 restraints weight = 18497.673| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.33 r_work: 0.2751 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3548 Z= 0.156 Angle : 0.512 4.798 4825 Z= 0.253 Chirality : 0.042 0.161 541 Planarity : 0.004 0.036 611 Dihedral : 9.971 68.351 637 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.27 % Allowed : 5.75 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.40), residues: 429 helix: -3.87 (0.65), residues: 32 sheet: 0.63 (0.47), residues: 131 loop : -1.32 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 50 HIS 0.001 0.001 HIS L 41 PHE 0.005 0.001 PHE L 101 TYR 0.009 0.001 TYR A 369 ARG 0.004 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4955 time to fit residues: 34.3740 Evaluate side-chains 59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.084805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067874 restraints weight = 18713.936| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.36 r_work: 0.2730 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3548 Z= 0.242 Angle : 0.517 6.641 4825 Z= 0.253 Chirality : 0.042 0.168 541 Planarity : 0.004 0.051 611 Dihedral : 8.905 58.538 637 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.06 % Favored : 93.71 % Rotamer: Outliers : 0.27 % Allowed : 8.22 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.41), residues: 429 helix: -3.76 (0.72), residues: 32 sheet: 0.02 (0.43), residues: 155 loop : -1.26 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.001 0.001 HIS L 40 PHE 0.007 0.001 PHE A 347 TYR 0.009 0.001 TYR A 369 ARG 0.007 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7439 (t0) cc_final: 0.7087 (t0) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4941 time to fit residues: 34.6145 Evaluate side-chains 59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.068158 restraints weight = 18793.329| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.39 r_work: 0.2733 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3548 Z= 0.199 Angle : 0.511 6.980 4825 Z= 0.250 Chirality : 0.042 0.214 541 Planarity : 0.004 0.053 611 Dihedral : 7.928 57.758 637 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.36 % Favored : 94.41 % Rotamer: Outliers : 0.27 % Allowed : 9.32 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.41), residues: 429 helix: -3.80 (0.69), residues: 32 sheet: 0.27 (0.45), residues: 146 loop : -1.28 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS L 41 PHE 0.005 0.001 PHE A 347 TYR 0.009 0.001 TYR A 369 ARG 0.005 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7454 (t0) cc_final: 0.7117 (t0) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.4714 time to fit residues: 32.1727 Evaluate side-chains 58 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068347 restraints weight = 18629.206| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.43 r_work: 0.2734 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3548 Z= 0.184 Angle : 0.505 6.845 4825 Z= 0.247 Chirality : 0.042 0.205 541 Planarity : 0.004 0.060 611 Dihedral : 7.256 56.937 637 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.13 % Favored : 94.64 % Rotamer: Outliers : 0.55 % Allowed : 9.32 % Favored : 90.14 % 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: -1.37 (0.41), residues: 429 helix: -3.78 (0.70), residues: 32 sheet: 0.18 (0.44), residues: 152 loop : -1.22 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.001 HIS L 41 PHE 0.006 0.001 PHE A 347 TYR 0.009 0.001 TYR A 369 ARG 0.006 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: H 73 ASP cc_start: 0.7445 (t0) cc_final: 0.7108 (t0) outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.4465 time to fit residues: 32.2496 Evaluate side-chains 61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.068392 restraints weight = 18656.207| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.43 r_work: 0.2737 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3548 Z= 0.174 Angle : 0.500 6.920 4825 Z= 0.245 Chirality : 0.042 0.193 541 Planarity : 0.004 0.057 611 Dihedral : 6.911 56.435 637 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.13 % Favored : 94.64 % Rotamer: Outliers : 0.55 % Allowed : 11.78 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.41), residues: 429 helix: -3.79 (0.69), residues: 32 sheet: 0.17 (0.44), residues: 152 loop : -1.21 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.001 HIS L 41 PHE 0.005 0.001 PHE A 400 TYR 0.009 0.001 TYR A 369 ARG 0.006 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8170 (m-10) outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.4638 time to fit residues: 31.8079 Evaluate side-chains 61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.087397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.069998 restraints weight = 18761.215| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.46 r_work: 0.2760 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3548 Z= 0.127 Angle : 0.491 6.516 4825 Z= 0.243 Chirality : 0.042 0.175 541 Planarity : 0.004 0.061 611 Dihedral : 6.599 56.356 637 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.73 % Favored : 96.04 % Rotamer: Outliers : 0.55 % Allowed : 12.33 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.41), residues: 429 helix: -3.75 (0.70), residues: 32 sheet: 0.42 (0.46), residues: 142 loop : -1.17 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS L 41 PHE 0.005 0.000 PHE A 338 TYR 0.009 0.001 TYR A 369 ARG 0.006 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: H 73 ASP cc_start: 0.7353 (t0) cc_final: 0.7095 (t0) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.4558 time to fit residues: 33.2734 Evaluate side-chains 61 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069224 restraints weight = 18686.511| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.43 r_work: 0.2753 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3548 Z= 0.166 Angle : 0.495 6.256 4825 Z= 0.243 Chirality : 0.041 0.164 541 Planarity : 0.004 0.061 611 Dihedral : 6.456 55.794 637 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.96 % Favored : 95.80 % Rotamer: Outliers : 0.27 % Allowed : 12.88 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.41), residues: 429 helix: -3.75 (0.71), residues: 32 sheet: 0.20 (0.44), residues: 152 loop : -1.17 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS L 41 PHE 0.005 0.001 PHE A 400 TYR 0.009 0.001 TYR A 369 ARG 0.008 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8306 (m-80) REVERT: H 73 ASP cc_start: 0.7364 (t0) cc_final: 0.7082 (t0) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.4636 time to fit residues: 31.1932 Evaluate side-chains 59 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.0870 chunk 11 optimal weight: 6.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.069447 restraints weight = 18771.137| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.44 r_work: 0.2757 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3548 Z= 0.154 Angle : 0.493 5.824 4825 Z= 0.244 Chirality : 0.041 0.158 541 Planarity : 0.004 0.064 611 Dihedral : 6.349 55.552 637 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 0.82 % Allowed : 12.60 % Favored : 86.58 % 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: -1.28 (0.42), residues: 429 helix: -3.75 (0.71), residues: 32 sheet: 0.22 (0.44), residues: 152 loop : -1.14 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS L 41 PHE 0.005 0.001 PHE A 400 TYR 0.009 0.001 TYR A 369 ARG 0.008 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: H 73 ASP cc_start: 0.7386 (t0) cc_final: 0.7094 (t0) outliers start: 3 outliers final: 1 residues processed: 60 average time/residue: 0.4799 time to fit residues: 33.3290 Evaluate side-chains 60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.069929 restraints weight = 18811.603| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.47 r_work: 0.2766 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3548 Z= 0.141 Angle : 0.497 5.439 4825 Z= 0.246 Chirality : 0.041 0.156 541 Planarity : 0.005 0.067 611 Dihedral : 6.218 55.341 637 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 0.55 % Allowed : 13.15 % Favored : 86.30 % 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: -1.19 (0.41), residues: 429 helix: -3.74 (0.71), residues: 32 sheet: 0.46 (0.46), residues: 142 loop : -1.15 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS L 41 PHE 0.005 0.001 PHE A 400 TYR 0.009 0.001 TYR A 369 ARG 0.009 0.001 ARG H 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: H 73 ASP cc_start: 0.7368 (t0) cc_final: 0.7113 (t0) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.4772 time to fit residues: 33.6734 Evaluate side-chains 60 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.088052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.070826 restraints weight = 18520.036| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.45 r_work: 0.2778 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3548 Z= 0.135 Angle : 0.494 5.199 4825 Z= 0.247 Chirality : 0.041 0.157 541 Planarity : 0.004 0.058 611 Dihedral : 6.093 55.217 637 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.73 % Favored : 96.04 % Rotamer: Outliers : 0.55 % Allowed : 13.70 % Favored : 85.75 % 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: -1.13 (0.42), residues: 429 helix: -3.77 (0.70), residues: 32 sheet: 0.53 (0.47), residues: 142 loop : -1.12 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS H 35 PHE 0.005 0.000 PHE A 338 TYR 0.009 0.001 TYR A 369 ARG 0.009 0.001 ARG H 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.10 seconds wall clock time: 67 minutes 58.44 seconds (4078.44 seconds total)