Starting phenix.real_space_refine on Tue Sep 24 03:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/09_2024/7x8w_33059_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/09_2024/7x8w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/09_2024/7x8w_33059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/09_2024/7x8w_33059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/09_2024/7x8w_33059_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/09_2024/7x8w_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.95, per 1000 atoms: 0.59 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: 2.01 Conformation dependent library (CDL) restraints added in 602.5 milliseconds 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: 0.85 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: 2.07 Time building geometry restraints manager: 2.35 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: 0.490 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: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.880 Find NCS groups from input model: 0.050 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.4600 time to fit residues: 36.6208 Evaluate side-chains 58 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 68.350 637 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 fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4896 time to fit residues: 33.9451 Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.0010 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3548 Z= 0.239 Angle : 0.516 6.615 4825 Z= 0.252 Chirality : 0.042 0.168 541 Planarity : 0.004 0.051 611 Dihedral : 8.935 58.644 637 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.83 % Favored : 93.94 % 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: -3.77 (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 41 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 fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7718 (t0) cc_final: 0.7425 (t0) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4606 time to fit residues: 32.0103 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3548 Z= 0.136 Angle : 0.501 6.829 4825 Z= 0.244 Chirality : 0.042 0.213 541 Planarity : 0.004 0.055 611 Dihedral : 7.886 58.255 637 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.90 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 8.49 % Favored : 91.23 % 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: -1.29 (0.41), residues: 429 helix: -3.79 (0.69), residues: 32 sheet: 0.66 (0.47), residues: 131 loop : -1.32 (0.38), residues: 266 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 0.004 0.000 PHE L 101 TYR 0.009 0.001 TYR A 369 ARG 0.006 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 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7650 (t0) cc_final: 0.7361 (t0) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4566 time to fit residues: 31.6709 Evaluate side-chains 57 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 30 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3548 Z= 0.144 Angle : 0.493 6.695 4825 Z= 0.241 Chirality : 0.042 0.207 541 Planarity : 0.004 0.057 611 Dihedral : 7.241 57.638 637 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.66 % Favored : 95.10 % Rotamer: Outliers : 0.55 % Allowed : 10.41 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.29 (0.41), residues: 429 helix: -3.75 (0.71), residues: 32 sheet: 0.31 (0.46), residues: 145 loop : -1.19 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.000 HIS L 41 PHE 0.004 0.000 PHE L 101 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 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8022 (m-10) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.4475 time to fit residues: 31.7760 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 10 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3548 Z= 0.323 Angle : 0.533 6.475 4825 Z= 0.264 Chirality : 0.042 0.198 541 Planarity : 0.004 0.057 611 Dihedral : 7.022 56.038 637 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.36 % Favored : 94.41 % Rotamer: Outliers : 0.55 % Allowed : 11.23 % Favored : 88.22 % 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: -1.49 (0.41), residues: 429 helix: -3.83 (0.70), residues: 32 sheet: 0.11 (0.44), residues: 152 loop : -1.32 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS L 40 PHE 0.012 0.001 PHE A 347 TYR 0.008 0.001 TYR A 369 ARG 0.006 0.001 ARG H 72 *********************** 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 fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8000 (m-10) REVERT: H 73 ASP cc_start: 0.7794 (t0) cc_final: 0.7434 (t0) outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.4412 time to fit residues: 30.2777 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3548 Z= 0.155 Angle : 0.499 6.570 4825 Z= 0.247 Chirality : 0.042 0.180 541 Planarity : 0.004 0.059 611 Dihedral : 6.784 56.127 637 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 0.82 % Allowed : 12.05 % 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: -1.36 (0.41), residues: 429 helix: -3.79 (0.70), residues: 32 sheet: 0.18 (0.44), residues: 152 loop : -1.20 (0.40), residues: 245 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 400 TYR 0.009 0.001 TYR A 369 ARG 0.007 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 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: H 73 ASP cc_start: 0.7671 (t0) cc_final: 0.7359 (t0) outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 0.4476 time to fit residues: 31.6884 Evaluate side-chains 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3548 Z= 0.134 Angle : 0.486 5.931 4825 Z= 0.241 Chirality : 0.041 0.160 541 Planarity : 0.004 0.065 611 Dihedral : 6.475 55.871 637 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.73 % Favored : 96.04 % Rotamer: Outliers : 0.82 % Allowed : 12.05 % 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: -1.29 (0.41), residues: 429 helix: -3.76 (0.71), residues: 32 sheet: 0.20 (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 0.001 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 106 *********************** 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 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 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: 0.8965 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: H 73 ASP cc_start: 0.7632 (t0) cc_final: 0.7364 (t0) REVERT: L 89 TYR cc_start: 0.8832 (m-80) cc_final: 0.8609 (m-80) outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 0.3997 time to fit residues: 28.6757 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP 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 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3548 Z= 0.243 Angle : 0.512 5.724 4825 Z= 0.252 Chirality : 0.041 0.160 541 Planarity : 0.004 0.064 611 Dihedral : 6.475 55.185 637 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.66 % Favored : 95.10 % Rotamer: Outliers : 1.10 % Allowed : 12.33 % 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: -1.38 (0.41), residues: 429 helix: -3.74 (0.72), residues: 32 sheet: 0.16 (0.44), residues: 152 loop : -1.23 (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 A 519 PHE 0.008 0.001 PHE A 347 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 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: H 73 ASP cc_start: 0.7713 (t0) cc_final: 0.7399 (t0) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.3920 time to fit residues: 27.6196 Evaluate side-chains 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS 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 20 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1531 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= 0.132 Angle : 0.494 5.425 4825 Z= 0.245 Chirality : 0.042 0.147 541 Planarity : 0.005 0.068 611 Dihedral : 6.330 55.338 637 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.73 % Favored : 96.04 % 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: -1.27 (0.41), residues: 429 helix: -3.71 (0.73), residues: 32 sheet: 0.19 (0.44), residues: 152 loop : -1.12 (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 338 TYR 0.009 0.001 TYR A 369 ARG 0.007 0.001 ARG H 106 ********************** 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 65 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: H 73 ASP cc_start: 0.7632 (t0) cc_final: 0.7356 (t0) REVERT: L 89 TYR cc_start: 0.8820 (m-80) cc_final: 0.8515 (m-80) outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.4825 time to fit residues: 34.5034 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP 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 29 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.087112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.069645 restraints weight = 18463.971| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.46 r_work: 0.2760 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3548 Z= 0.139 Angle : 0.489 4.895 4825 Z= 0.243 Chirality : 0.041 0.155 541 Planarity : 0.005 0.066 611 Dihedral : 6.187 55.104 637 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 0.82 % Allowed : 12.88 % 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: -1.25 (0.41), residues: 429 helix: -3.73 (0.72), residues: 32 sheet: 0.22 (0.44), residues: 152 loop : -1.11 (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 H 35 PHE 0.005 0.001 PHE A 400 TYR 0.009 0.001 TYR A 369 ARG 0.009 0.001 ARG H 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.02 seconds wall clock time: 50 minutes 47.12 seconds (3047.12 seconds total)