Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:49:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/04_2023/6wyk_21967.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/04_2023/6wyk_21967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/04_2023/6wyk_21967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/04_2023/6wyk_21967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/04_2023/6wyk_21967.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/04_2023/6wyk_21967.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2029 2.51 5 N 490 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3083 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3083 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain breaks: 1 Time building chain proxies: 2.23, per 1000 atoms: 0.72 Number of scatterers: 3083 At special positions: 0 Unit cell: (73.95, 70.992, 76.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 546 8.00 N 490 7.00 C 2029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 479.4 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 13 through 29 removed outlier: 4.045A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 78 Proline residue: A 45 - end of helix removed outlier: 3.508A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.530A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 79 through 108 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.510A pdb=" N ILE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.671A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.268A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.025A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.780A pdb=" N GLN A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 255 removed outlier: 3.832A pdb=" N GLU A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 4.420A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 removed outlier: 4.021A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.388A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.667A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 946 1.34 - 1.46: 451 1.46 - 1.57: 1705 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3136 Sorted by residual: bond pdb=" N VAL A 225 " pdb=" CA VAL A 225 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.33e-02 5.65e+03 1.29e+01 bond pdb=" N VAL A 274 " pdb=" CA VAL A 274 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.53e+00 bond pdb=" N LYS A 223 " pdb=" CA LYS A 223 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.31e-02 5.83e+03 9.29e+00 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.460 1.497 -0.036 1.26e-02 6.30e+03 8.36e+00 bond pdb=" N ASN A 148 " pdb=" CA ASN A 148 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.37e+00 ... (remaining 3131 not shown) Histogram of bond angle deviations from ideal: 98.27 - 104.90: 65 104.90 - 111.52: 1514 111.52 - 118.15: 932 118.15 - 124.77: 1733 124.77 - 131.40: 25 Bond angle restraints: 4269 Sorted by residual: angle pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 120.57 115.75 4.82 1.07e+00 8.73e-01 2.03e+01 angle pdb=" CA GLN A 150 " pdb=" C GLN A 150 " pdb=" O GLN A 150 " ideal model delta sigma weight residual 120.32 115.83 4.49 1.11e+00 8.12e-01 1.64e+01 angle pdb=" CA VAL A 274 " pdb=" C VAL A 274 " pdb=" O VAL A 274 " ideal model delta sigma weight residual 120.85 116.85 4.00 1.06e+00 8.90e-01 1.43e+01 angle pdb=" CA THR A 275 " pdb=" C THR A 275 " pdb=" O THR A 275 " ideal model delta sigma weight residual 119.97 115.76 4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" CA PHE A 273 " pdb=" C PHE A 273 " pdb=" O PHE A 273 " ideal model delta sigma weight residual 120.82 117.24 3.58 1.05e+00 9.07e-01 1.16e+01 ... (remaining 4264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 1699 15.92 - 31.83: 138 31.83 - 47.75: 26 47.75 - 63.66: 2 63.66 - 79.58: 1 Dihedral angle restraints: 1866 sinusoidal: 685 harmonic: 1181 Sorted by residual: dihedral pdb=" CA ILE A 73 " pdb=" C ILE A 73 " pdb=" N SER A 74 " pdb=" CA SER A 74 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO A 109 " pdb=" C PRO A 109 " pdb=" N GLY A 110 " pdb=" CA GLY A 110 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N VAL A 222 " pdb=" CA VAL A 222 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 411 0.053 - 0.106: 109 0.106 - 0.159: 13 0.159 - 0.212: 3 0.212 - 0.266: 2 Chirality restraints: 538 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL A 225 " pdb=" CA VAL A 225 " pdb=" CG1 VAL A 225 " pdb=" CG2 VAL A 225 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLN A 150 " pdb=" N GLN A 150 " pdb=" C GLN A 150 " pdb=" CB GLN A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 535 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 147 " 0.015 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C ALA A 147 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 147 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 148 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.022 2.00e-02 2.50e+03 1.80e-02 6.46e+00 pdb=" CG TYR A 299 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 224 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C VAL A 224 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 224 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 225 " 0.013 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 560 2.76 - 3.29: 3550 3.29 - 3.83: 4990 3.83 - 4.36: 5548 4.36 - 4.90: 9361 Nonbonded interactions: 24009 Sorted by model distance: nonbonded pdb=" O ALA A 71 " pdb=" OG1 THR A 166 " model vdw 2.223 2.440 nonbonded pdb=" O SER A 278 " pdb=" OG1 THR A 281 " model vdw 2.294 2.440 nonbonded pdb=" O VAL A 151 " pdb=" OG1 THR A 154 " model vdw 2.309 2.440 nonbonded pdb=" O LEU A 228 " pdb=" OG1 THR A 232 " model vdw 2.383 2.440 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 415 " model vdw 2.387 2.440 ... (remaining 24004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.550 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 : 0.007 0.057 3136 Z= 0.471 Angle : 0.769 5.594 4269 Z= 0.463 Chirality : 0.048 0.266 538 Planarity : 0.005 0.029 524 Dihedral : 11.978 79.581 1116 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.34), residues: 412 helix: -1.19 (0.24), residues: 321 sheet: None (None), residues: 0 loop : -2.03 (0.57), residues: 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.324 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1539 time to fit residues: 20.9654 Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3136 Z= 0.218 Angle : 0.660 5.929 4269 Z= 0.336 Chirality : 0.042 0.151 538 Planarity : 0.004 0.026 524 Dihedral : 5.360 25.429 441 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 2.76 % 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: 0.81 (0.39), residues: 412 helix: 1.17 (0.27), residues: 328 sheet: None (None), residues: 0 loop : -1.88 (0.57), residues: 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.309 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.1112 time to fit residues: 12.6185 Evaluate side-chains 84 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0333 time to fit residues: 0.7869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3136 Z= 0.219 Angle : 0.654 8.226 4269 Z= 0.327 Chirality : 0.043 0.172 538 Planarity : 0.003 0.023 524 Dihedral : 5.203 29.976 441 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.41), residues: 412 helix: 1.61 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.80 (0.58), residues: 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.321 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.1193 time to fit residues: 13.4561 Evaluate side-chains 78 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0327 time to fit residues: 0.6540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3136 Z= 0.241 Angle : 0.668 9.567 4269 Z= 0.326 Chirality : 0.043 0.157 538 Planarity : 0.003 0.024 524 Dihedral : 5.185 29.535 441 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.76 % 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: 1.60 (0.41), residues: 412 helix: 1.71 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.61 (0.60), residues: 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.324 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.1175 time to fit residues: 12.5917 Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0516 time to fit residues: 1.1012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 3136 Z= 0.216 Angle : 0.654 10.284 4269 Z= 0.324 Chirality : 0.044 0.159 538 Planarity : 0.004 0.043 524 Dihedral : 5.124 29.101 441 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.53 % 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: 1.62 (0.41), residues: 412 helix: 1.68 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.39 (0.62), residues: 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.367 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 80 average time/residue: 0.1219 time to fit residues: 12.3551 Evaluate side-chains 80 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0374 time to fit residues: 0.7623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3136 Z= 0.223 Angle : 0.671 10.868 4269 Z= 0.330 Chirality : 0.044 0.167 538 Planarity : 0.003 0.024 524 Dihedral : 5.088 29.335 441 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.84 % 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: 1.61 (0.41), residues: 412 helix: 1.66 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.34 (0.65), residues: 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.344 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 80 average time/residue: 0.1174 time to fit residues: 12.0452 Evaluate side-chains 77 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0347 time to fit residues: 0.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7678 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3136 Z= 0.222 Angle : 0.720 12.154 4269 Z= 0.346 Chirality : 0.045 0.204 538 Planarity : 0.004 0.050 524 Dihedral : 5.137 29.003 441 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.92 % 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: 1.59 (0.41), residues: 412 helix: 1.63 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.32 (0.65), residues: 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.348 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 78 average time/residue: 0.1328 time to fit residues: 13.0372 Evaluate side-chains 78 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0404 time to fit residues: 0.6759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.7651 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 3136 Z= 0.215 Angle : 0.721 13.743 4269 Z= 0.346 Chirality : 0.045 0.228 538 Planarity : 0.003 0.024 524 Dihedral : 5.079 29.257 441 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.53 % 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: 1.75 (0.42), residues: 412 helix: 1.75 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.06 (0.68), residues: 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.354 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 89 average time/residue: 0.1284 time to fit residues: 14.3112 Evaluate side-chains 86 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0340 time to fit residues: 0.7838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 3136 Z= 0.238 Angle : 0.791 16.468 4269 Z= 0.370 Chirality : 0.046 0.233 538 Planarity : 0.004 0.051 524 Dihedral : 5.181 29.168 441 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.41), residues: 412 helix: 1.65 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.06 (0.68), residues: 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.350 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.1310 time to fit residues: 13.8108 Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 3136 Z= 0.203 Angle : 0.775 14.733 4269 Z= 0.363 Chirality : 0.046 0.233 538 Planarity : 0.004 0.046 524 Dihedral : 5.110 28.652 441 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.42), residues: 412 helix: 1.70 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.12 (0.67), residues: 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.297 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.1251 time to fit residues: 13.8116 Evaluate side-chains 87 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0395 time to fit residues: 0.6137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131510 restraints weight = 5722.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134175 restraints weight = 3794.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136008 restraints weight = 2881.049| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3136 Z= 0.207 Angle : 0.814 14.640 4269 Z= 0.380 Chirality : 0.046 0.225 538 Planarity : 0.004 0.041 524 Dihedral : 5.102 28.363 441 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.42), residues: 412 helix: 1.64 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -1.11 (0.67), residues: 88 =============================================================================== Job complete usr+sys time: 1030.23 seconds wall clock time: 19 minutes 3.78 seconds (1143.78 seconds total)