Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:46:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/11_2022/7lto_23517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/11_2022/7lto_23517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/11_2022/7lto_23517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/11_2022/7lto_23517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/11_2022/7lto_23517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/11_2022/7lto_23517.pdb" } resolution = 3.2 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4754 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2876 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain breaks: 4 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain breaks: 5 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.11, per 1000 atoms: 0.65 Number of scatterers: 4754 At special positions: 0 Unit cell: (64.904, 77.672, 101.08, 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 26 16.00 O 838 8.00 N 776 7.00 C 3114 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: 1.86 Conformation dependent library (CDL) restraints added in 702.9 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 58.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.660A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.793A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.971A pdb=" N VAL A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.030A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.775A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.920A pdb=" N CYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.985A pdb=" N GLN A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.714A pdb=" N PHE A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 4.329A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.936A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.550A pdb=" N GLU A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.569A pdb=" N ASP A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.513A pdb=" N MET B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.541A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.065A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.663A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 4.018A pdb=" N LEU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 609 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: 1.04 Time building geometry restraints manager: 2.03 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: 1470 1.34 - 1.46: 861 1.46 - 1.58: 2484 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4853 Sorted by residual: bond pdb=" CA GLU A 193 " pdb=" C GLU A 193 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.24e-02 6.50e+03 6.64e+00 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.25e-02 6.40e+03 3.33e+00 bond pdb=" CA ALA B 323 " pdb=" C ALA B 323 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.23e-02 6.61e+03 2.58e+00 bond pdb=" C MET A 241 " pdb=" O MET A 241 " ideal model delta sigma weight residual 1.244 1.228 0.016 1.00e-02 1.00e+04 2.43e+00 bond pdb=" C TRP A 240 " pdb=" O TRP A 240 " ideal model delta sigma weight residual 1.236 1.219 0.018 1.29e-02 6.01e+03 1.85e+00 ... (remaining 4848 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.90: 112 106.90 - 113.71: 2677 113.71 - 120.53: 1949 120.53 - 127.34: 1787 127.34 - 134.16: 38 Bond angle restraints: 6563 Sorted by residual: angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 112.57 119.12 -6.55 1.13e+00 7.83e-01 3.36e+01 angle pdb=" N TRP A 240 " pdb=" CA TRP A 240 " pdb=" C TRP A 240 " ideal model delta sigma weight residual 112.23 119.19 -6.96 1.26e+00 6.30e-01 3.06e+01 angle pdb=" C ASP A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 119.24 124.34 -5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 114.09 106.86 7.23 1.55e+00 4.16e-01 2.17e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 112.04 105.82 6.22 1.44e+00 4.82e-01 1.86e+01 ... (remaining 6558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2596 17.82 - 35.64: 241 35.64 - 53.46: 58 53.46 - 71.28: 10 71.28 - 89.11: 5 Dihedral angle restraints: 2910 sinusoidal: 1106 harmonic: 1804 Sorted by residual: dihedral pdb=" CA GLU B 398 " pdb=" C GLU B 398 " pdb=" N PHE B 399 " pdb=" CA PHE B 399 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA SER A 411 " pdb=" C SER A 411 " pdb=" N TYR A 412 " pdb=" CA TYR A 412 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN B 345 " pdb=" C ASN B 345 " pdb=" N SER B 346 " pdb=" CA SER B 346 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 695 0.075 - 0.150: 54 0.150 - 0.225: 7 0.225 - 0.299: 3 0.299 - 0.374: 1 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA TRP A 240 " pdb=" N TRP A 240 " pdb=" C TRP A 240 " pdb=" CB TRP A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA TYR A 81 " pdb=" N TYR A 81 " pdb=" C TYR A 81 " pdb=" CB TYR A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR A 82 " pdb=" N TYR A 82 " pdb=" C TYR A 82 " pdb=" CB TYR A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 757 not shown) Planarity restraints: 819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 193 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU A 193 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 193 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 411 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A 411 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 411 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 412 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 239 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ILE A 239 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 239 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 240 " -0.009 2.00e-02 2.50e+03 ... (remaining 816 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 929 2.77 - 3.30: 4572 3.30 - 3.83: 7256 3.83 - 4.37: 9095 4.37 - 4.90: 15381 Nonbonded interactions: 37233 Sorted by model distance: nonbonded pdb=" O PHE A 50 " pdb=" NE2 GLN A 54 " model vdw 2.232 2.520 nonbonded pdb=" O ARG A 387 " pdb=" OG SER A 391 " model vdw 2.281 2.440 nonbonded pdb=" O LYS A 343 " pdb=" OG SER A 347 " model vdw 2.282 2.440 nonbonded pdb=" NZ LYS A 207 " pdb=" O VAL A 321 " model vdw 2.311 2.520 nonbonded pdb=" NE2 GLN B 370 " pdb=" O THR B 414 " model vdw 2.311 2.520 ... (remaining 37228 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3114 2.51 5 N 776 2.21 5 O 838 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.900 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: 4.990 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 16.960 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.003 0.032 4853 Z= 0.219 Angle : 0.707 7.229 6563 Z= 0.447 Chirality : 0.049 0.374 760 Planarity : 0.003 0.037 819 Dihedral : 15.408 89.105 1726 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 3.25 % 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: -4.26 (0.29), residues: 583 helix: -2.13 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -3.81 (0.31), residues: 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.451 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.1740 time to fit residues: 24.2446 Evaluate side-chains 87 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0535 time to fit residues: 1.7927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 90 ASN A 94 ASN A 134 GLN A 345 GLN A 383 GLN B 201 HIS B 206 ASN B 211 GLN B 277 ASN B 389 GLN B 407 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4853 Z= 0.198 Angle : 0.566 6.644 6563 Z= 0.289 Chirality : 0.040 0.147 760 Planarity : 0.004 0.041 819 Dihedral : 4.618 20.652 640 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 1.83 % 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: -2.75 (0.32), residues: 583 helix: -0.75 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -3.52 (0.32), residues: 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.592 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 0.1478 time to fit residues: 18.1566 Evaluate side-chains 85 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0466 time to fit residues: 1.1283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.0000 chunk 16 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.0070 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 4853 Z= 0.143 Angle : 0.518 6.499 6563 Z= 0.259 Chirality : 0.038 0.125 760 Planarity : 0.003 0.042 819 Dihedral : 4.271 17.783 640 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 2.44 % 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: -1.74 (0.34), residues: 583 helix: 0.08 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.16 (0.33), residues: 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.577 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.1440 time to fit residues: 19.3440 Evaluate side-chains 97 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0539 time to fit residues: 1.3650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.0040 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 4853 Z= 0.150 Angle : 0.532 9.616 6563 Z= 0.261 Chirality : 0.039 0.142 760 Planarity : 0.003 0.045 819 Dihedral : 4.118 18.471 640 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 1.83 % 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 (0.35), residues: 583 helix: 0.42 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -2.86 (0.34), residues: 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.567 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 0.1378 time to fit residues: 17.5309 Evaluate side-chains 89 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0431 time to fit residues: 1.0769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 48 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.0060 chunk 51 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 508 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 4853 Z= 0.134 Angle : 0.533 11.428 6563 Z= 0.260 Chirality : 0.039 0.128 760 Planarity : 0.003 0.042 819 Dihedral : 3.981 18.542 640 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer Outliers : 1.63 % 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: -0.96 (0.35), residues: 583 helix: 0.69 (0.30), residues: 347 sheet: None (None), residues: 0 loop : -2.78 (0.35), residues: 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.1457 time to fit residues: 19.8598 Evaluate side-chains 91 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0580 time to fit residues: 1.2973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 508 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4853 Z= 0.193 Angle : 0.599 15.733 6563 Z= 0.289 Chirality : 0.040 0.130 760 Planarity : 0.003 0.043 819 Dihedral : 4.139 19.810 640 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.35), residues: 583 helix: 0.71 (0.30), residues: 344 sheet: None (None), residues: 0 loop : -2.70 (0.35), residues: 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.624 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 88 average time/residue: 0.1500 time to fit residues: 17.5182 Evaluate side-chains 86 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0469 time to fit residues: 1.2343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 508 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 4853 Z= 0.157 Angle : 0.566 14.840 6563 Z= 0.274 Chirality : 0.039 0.128 760 Planarity : 0.003 0.044 819 Dihedral : 4.050 19.456 640 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.81 % 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: -0.72 (0.35), residues: 583 helix: 0.85 (0.30), residues: 345 sheet: None (None), residues: 0 loop : -2.60 (0.35), residues: 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.597 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 0.1481 time to fit residues: 17.8369 Evaluate side-chains 85 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0565 time to fit residues: 1.0830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 52 optimal weight: 0.2980 chunk 31 optimal weight: 0.1980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4853 Z= 0.135 Angle : 0.599 15.333 6563 Z= 0.280 Chirality : 0.040 0.196 760 Planarity : 0.003 0.042 819 Dihedral : 3.787 19.310 640 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.20 % 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: -0.50 (0.36), residues: 583 helix: 1.02 (0.30), residues: 350 sheet: None (None), residues: 0 loop : -2.57 (0.36), residues: 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.617 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1473 time to fit residues: 18.3892 Evaluate side-chains 87 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0392 time to fit residues: 0.7575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 4853 Z= 0.145 Angle : 0.608 13.553 6563 Z= 0.286 Chirality : 0.041 0.227 760 Planarity : 0.003 0.044 819 Dihedral : 3.793 19.634 640 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 0.20 % 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: -0.54 (0.36), residues: 583 helix: 0.95 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.59 (0.36), residues: 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.589 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.1346 time to fit residues: 16.3224 Evaluate side-chains 89 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0687 time to fit residues: 0.8420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4853 Z= 0.207 Angle : 0.674 15.185 6563 Z= 0.317 Chirality : 0.043 0.242 760 Planarity : 0.004 0.041 819 Dihedral : 4.083 19.398 640 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 0.20 % 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: -0.65 (0.35), residues: 583 helix: 0.88 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -2.59 (0.36), residues: 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.598 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.1454 time to fit residues: 16.3803 Evaluate side-chains 86 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0656 time to fit residues: 1.0660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159609 restraints weight = 6106.255| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.45 r_work: 0.3974 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work: 0.3942 rms_B_bonded: 1.59 restraints_weight: 0.1250 r_work: 0.3918 rms_B_bonded: 1.95 restraints_weight: 0.0625 r_work: 0.3886 rms_B_bonded: 2.52 restraints_weight: 0.0312 r_work: 0.3840 rms_B_bonded: 3.40 restraints_weight: 0.0156 r_work: 0.3770 rms_B_bonded: 4.88 restraints_weight: 0.0078 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4853 Z= 0.199 Angle : 0.659 14.043 6563 Z= 0.312 Chirality : 0.042 0.240 760 Planarity : 0.003 0.041 819 Dihedral : 4.112 19.338 640 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 1.02 % 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: -0.66 (0.35), residues: 583 helix: 0.82 (0.29), residues: 350 sheet: None (None), residues: 0 loop : -2.50 (0.37), residues: 233 =============================================================================== Job complete usr+sys time: 1256.50 seconds wall clock time: 23 minutes 41.35 seconds (1421.35 seconds total)