Starting phenix.real_space_refine on Mon Oct 14 17:38:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pth_17871/10_2024/8pth_17871.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pth_17871/10_2024/8pth_17871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pth_17871/10_2024/8pth_17871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pth_17871/10_2024/8pth_17871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pth_17871/10_2024/8pth_17871.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pth_17871/10_2024/8pth_17871.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 27 5.49 5 S 54 5.16 5 C 5715 2.51 5 N 1629 2.21 5 O 1819 1.98 5 H 8991 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18236 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 7856 Classifications: {'peptide': 509} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 1 Chain: "C" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2868 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain breaks: 1 Chain: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain breaks: 1 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 47.327 53.573 19.817 1.00 43.06 S ATOM 4472 SG CYS A 282 45.157 52.027 16.924 1.00 58.28 S Time building chain proxies: 8.52, per 1000 atoms: 0.47 Number of scatterers: 18236 At special positions: 0 Unit cell: (89.88, 94.92, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 27 15.00 O 1819 8.00 N 1629 7.00 C 5715 6.00 H 8991 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " Number of angles added : 1 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 13 sheets defined 43.4% alpha, 11.9% beta 7 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.661A pdb=" N CYS A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.600A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.530A pdb=" N GLU A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.404A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.598A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.875A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.696A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 161 through 183 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.737A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.854A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.751A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.006A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.393A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.660A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.660A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.869A pdb=" N CYS B 142 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 213 removed outlier: 3.534A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 385 through 388 removed outlier: 6.714A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 414 " --> pdb=" O CYS C 409 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 5.59 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8961 1.03 - 1.23: 40 1.23 - 1.42: 3972 1.42 - 1.61: 5420 1.61 - 1.81: 76 Bond restraints: 18469 Sorted by residual: bond pdb=" N LYS C 40 " pdb=" CA LYS C 40 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.28e-02 6.10e+03 6.66e+00 bond pdb=" N LYS C 40 " pdb=" H LYS C 40 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" CA LYS C 40 " pdb=" C LYS C 40 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.40e-02 5.10e+03 1.02e+00 bond pdb=" C LYS C 40 " pdb=" O LYS C 40 " ideal model delta sigma weight residual 1.235 1.247 -0.012 1.26e-02 6.30e+03 9.30e-01 bond pdb=" NZ LYS C 40 " pdb=" HZ2 LYS C 40 " ideal model delta sigma weight residual 0.890 0.908 -0.018 2.00e-02 2.50e+03 7.83e-01 ... (remaining 18464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 32740 1.41 - 2.81: 561 2.81 - 4.22: 60 4.22 - 5.63: 0 5.63 - 7.03: 1 Bond angle restraints: 33362 Sorted by residual: angle pdb=" C LEU A 300 " pdb=" N ASP A 301 " pdb=" CA ASP A 301 " ideal model delta sigma weight residual 120.49 127.52 -7.03 1.42e+00 4.96e-01 2.45e+01 angle pdb=" CA LYS C 40 " pdb=" C LYS C 40 " pdb=" O LYS C 40 " ideal model delta sigma weight residual 120.80 117.99 2.81 1.08e+00 8.57e-01 6.78e+00 angle pdb=" CB LYS C 25 " pdb=" CG LYS C 25 " pdb=" CD LYS C 25 " ideal model delta sigma weight residual 111.30 115.15 -3.85 2.30e+00 1.89e-01 2.80e+00 angle pdb=" C ARG C 39 " pdb=" N LYS C 40 " pdb=" CA LYS C 40 " ideal model delta sigma weight residual 121.26 123.90 -2.64 1.59e+00 3.96e-01 2.75e+00 angle pdb=" C SER B 160 " pdb=" N HIS B 161 " pdb=" CA HIS B 161 " ideal model delta sigma weight residual 120.68 123.19 -2.51 1.52e+00 4.33e-01 2.73e+00 ... (remaining 33357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7634 17.91 - 35.81: 722 35.81 - 53.72: 251 53.72 - 71.63: 86 71.63 - 89.53: 18 Dihedral angle restraints: 8711 sinusoidal: 4994 harmonic: 3717 Sorted by residual: dihedral pdb=" CB GLU B 72 " pdb=" CG GLU B 72 " pdb=" CD GLU B 72 " pdb=" OE1 GLU B 72 " ideal model delta sinusoidal sigma weight residual 0.00 89.53 -89.53 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 248 " pdb=" CD ARG B 248 " pdb=" NE ARG B 248 " pdb=" CZ ARG B 248 " ideal model delta sinusoidal sigma weight residual 180.00 -135.33 -44.67 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU B 29 " pdb=" CG GLU B 29 " pdb=" CD GLU B 29 " pdb=" OE1 GLU B 29 " ideal model delta sinusoidal sigma weight residual 0.00 88.95 -88.95 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 947 0.027 - 0.053: 371 0.053 - 0.080: 78 0.080 - 0.106: 52 0.106 - 0.133: 26 Chirality restraints: 1474 Sorted by residual: chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 275 " pdb=" N VAL A 275 " pdb=" C VAL A 275 " pdb=" CB VAL A 275 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL B 86 " pdb=" N VAL B 86 " pdb=" C VAL B 86 " pdb=" CB VAL B 86 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1471 not shown) Planarity restraints: 2629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 301 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO A 302 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 429 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 430 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.018 2.00e-02 2.50e+03 7.22e-03 1.69e+00 pdb=" N9 A V 4 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" H8 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " -0.002 2.00e-02 2.50e+03 ... (remaining 2626 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.02: 173 2.02 - 2.66: 25960 2.66 - 3.31: 53063 3.31 - 3.95: 70121 3.95 - 4.60: 109135 Nonbonded interactions: 258452 Sorted by model distance: nonbonded pdb=" HB2 ALA A 268 " pdb="HD13 LEU C 31 " model vdw 1.375 2.440 nonbonded pdb=" OG1 THR B 97 " pdb=" HE2 HIS C 22 " model vdw 1.598 2.450 nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.605 2.450 nonbonded pdb="HH12 ARG A 24 " pdb=" OE2 GLU A 85 " model vdw 1.611 2.450 nonbonded pdb=" H21 G D 28 " pdb=" O2 C V 13 " model vdw 1.613 2.450 ... (remaining 258447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.370 Extract box with map and model: 0.250 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 46.000 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 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 : 0.002 0.033 9478 Z= 0.140 Angle : 0.438 7.033 12925 Z= 0.231 Chirality : 0.035 0.133 1474 Planarity : 0.003 0.038 1563 Dihedral : 17.857 89.534 3729 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.88 % Allowed : 20.23 % Favored : 77.89 % 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 (0.26), residues: 1094 helix: 2.19 (0.25), residues: 438 sheet: -0.49 (0.56), residues: 92 loop : -0.39 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.006 0.001 PHE C 44 TYR 0.009 0.001 TYR A 403 ARG 0.006 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.675 Fit side-chains REVERT: B 327 LEU cc_start: 0.8461 (tt) cc_final: 0.7966 (pp) outliers start: 18 outliers final: 16 residues processed: 121 average time/residue: 2.7621 time to fit residues: 360.5401 Evaluate side-chains 112 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 155 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9478 Z= 0.206 Angle : 0.469 4.132 12925 Z= 0.248 Chirality : 0.036 0.142 1474 Planarity : 0.004 0.053 1563 Dihedral : 11.987 73.578 1630 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.98 % Allowed : 19.40 % Favored : 78.62 % 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: 0.97 (0.26), residues: 1094 helix: 2.24 (0.25), residues: 441 sheet: -0.71 (0.50), residues: 112 loop : -0.39 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.456 Fit side-chains REVERT: B 148 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: C 88 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7266 (mp10) outliers start: 19 outliers final: 9 residues processed: 112 average time/residue: 2.5575 time to fit residues: 309.4940 Evaluate side-chains 114 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 155 GLN B 56 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9478 Z= 0.263 Angle : 0.484 5.308 12925 Z= 0.257 Chirality : 0.037 0.145 1474 Planarity : 0.004 0.051 1563 Dihedral : 11.862 73.627 1617 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.88 % Allowed : 19.60 % Favored : 78.52 % 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 (0.26), residues: 1094 helix: 2.09 (0.25), residues: 442 sheet: -0.94 (0.53), residues: 100 loop : -0.44 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.006 0.001 HIS B 174 PHE 0.013 0.001 PHE C 44 TYR 0.015 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.463 Fit side-chains REVERT: B 148 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: C 83 ARG cc_start: 0.7356 (tmm-80) cc_final: 0.7007 (tmm-80) REVERT: C 88 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: C 89 GLU cc_start: 0.7626 (mp0) cc_final: 0.7415 (mm-30) outliers start: 18 outliers final: 9 residues processed: 118 average time/residue: 2.6424 time to fit residues: 334.8471 Evaluate side-chains 110 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9478 Z= 0.186 Angle : 0.452 3.980 12925 Z= 0.239 Chirality : 0.036 0.144 1474 Planarity : 0.004 0.056 1563 Dihedral : 11.746 73.589 1617 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.29 % Allowed : 18.98 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1094 helix: 2.13 (0.25), residues: 442 sheet: -0.85 (0.58), residues: 88 loop : -0.49 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.335 Fit side-chains REVERT: A 301 ASP cc_start: 0.7922 (t0) cc_final: 0.7597 (t0) REVERT: B 20 MET cc_start: 0.8368 (mtt) cc_final: 0.8094 (mtt) REVERT: C 83 ARG cc_start: 0.7376 (tmm-80) cc_final: 0.7028 (tmm-80) REVERT: C 88 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7347 (mp10) outliers start: 22 outliers final: 9 residues processed: 118 average time/residue: 2.4813 time to fit residues: 315.6398 Evaluate side-chains 116 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 87 GLN A 271 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9478 Z= 0.268 Angle : 0.486 5.550 12925 Z= 0.257 Chirality : 0.037 0.144 1474 Planarity : 0.004 0.072 1563 Dihedral : 11.758 73.642 1617 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.88 % Allowed : 19.50 % Favored : 78.62 % 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: 0.70 (0.25), residues: 1094 helix: 2.00 (0.25), residues: 442 sheet: -1.02 (0.52), residues: 100 loop : -0.49 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.006 0.001 HIS B 174 PHE 0.013 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.006 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.442 Fit side-chains REVERT: A 84 GLN cc_start: 0.7590 (tt0) cc_final: 0.7357 (tp40) REVERT: B 148 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7595 (pm20) REVERT: C 83 ARG cc_start: 0.7342 (tmm-80) cc_final: 0.6975 (tmm-80) REVERT: C 88 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7171 (mp10) outliers start: 18 outliers final: 11 residues processed: 117 average time/residue: 2.5127 time to fit residues: 317.8203 Evaluate side-chains 115 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 87 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9478 Z= 0.252 Angle : 0.484 4.983 12925 Z= 0.255 Chirality : 0.037 0.145 1474 Planarity : 0.004 0.058 1563 Dihedral : 11.756 73.640 1617 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.88 % Allowed : 20.02 % Favored : 78.10 % 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: 0.70 (0.25), residues: 1094 helix: 2.01 (0.25), residues: 442 sheet: -0.95 (0.58), residues: 88 loop : -0.54 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.012 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.447 Fit side-chains REVERT: B 148 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: C 83 ARG cc_start: 0.7367 (tmm-80) cc_final: 0.7005 (tmm-80) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 2.3734 time to fit residues: 284.5774 Evaluate side-chains 115 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 87 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9478 Z= 0.261 Angle : 0.491 5.147 12925 Z= 0.259 Chirality : 0.037 0.145 1474 Planarity : 0.004 0.050 1563 Dihedral : 11.772 73.617 1617 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.09 % Allowed : 19.71 % Favored : 78.21 % 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: 0.69 (0.25), residues: 1094 helix: 1.97 (0.25), residues: 442 sheet: -0.83 (0.59), residues: 86 loop : -0.55 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.012 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.482 Fit side-chains REVERT: A 122 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 148 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 327 LEU cc_start: 0.8483 (tt) cc_final: 0.8049 (pp) REVERT: C 83 ARG cc_start: 0.7361 (tmm-80) cc_final: 0.6996 (tmm-80) outliers start: 20 outliers final: 10 residues processed: 111 average time/residue: 2.4622 time to fit residues: 294.8032 Evaluate side-chains 115 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 87 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9478 Z= 0.267 Angle : 0.493 5.137 12925 Z= 0.260 Chirality : 0.037 0.146 1474 Planarity : 0.004 0.054 1563 Dihedral : 11.749 73.669 1616 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.19 % Allowed : 19.29 % Favored : 78.52 % 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 (0.25), residues: 1094 helix: 1.94 (0.25), residues: 442 sheet: -0.87 (0.58), residues: 86 loop : -0.56 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: B 148 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: B 339 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: C 83 ARG cc_start: 0.7343 (tmm-80) cc_final: 0.6996 (tmm-80) outliers start: 21 outliers final: 12 residues processed: 111 average time/residue: 2.6043 time to fit residues: 313.7392 Evaluate side-chains 120 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 87 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9478 Z= 0.183 Angle : 0.463 4.783 12925 Z= 0.244 Chirality : 0.036 0.144 1474 Planarity : 0.004 0.057 1563 Dihedral : 11.674 75.323 1616 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.36 % Allowed : 20.44 % Favored : 78.21 % 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: 0.77 (0.26), residues: 1094 helix: 2.07 (0.25), residues: 442 sheet: -0.83 (0.59), residues: 86 loop : -0.53 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.008 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 THR cc_start: 0.8915 (m) cc_final: 0.8597 (m) REVERT: B 148 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: B 339 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: C 83 ARG cc_start: 0.7332 (tmm-80) cc_final: 0.7002 (tmm-80) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 2.4351 time to fit residues: 294.7119 Evaluate side-chains 119 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 87 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9478 Z= 0.290 Angle : 0.500 4.837 12925 Z= 0.265 Chirality : 0.038 0.144 1474 Planarity : 0.004 0.059 1563 Dihedral : 11.740 73.691 1615 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.36 % Allowed : 20.54 % Favored : 78.10 % 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: 0.64 (0.26), residues: 1094 helix: 1.94 (0.25), residues: 442 sheet: -0.89 (0.59), residues: 86 loop : -0.57 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.014 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.004 0.000 ARG B 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: B 148 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: B 339 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8205 (m-30) REVERT: C 83 ARG cc_start: 0.7334 (tmm-80) cc_final: 0.6986 (tmm-80) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 2.5839 time to fit residues: 303.0565 Evaluate side-chains 119 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.0030 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.084032 restraints weight = 34876.169| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.75 r_work: 0.2774 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1339 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: