Starting phenix.real_space_refine on Mon Jun 16 08:44:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pth_17871/06_2025/8pth_17871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pth_17871/06_2025/8pth_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/cci-nas-00/data/ceres_data/8pth_17871/06_2025/8pth_17871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pth_17871/06_2025/8pth_17871.map" model { file = "/net/cci-nas-00/data/ceres_data/8pth_17871/06_2025/8pth_17871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pth_17871/06_2025/8pth_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.68, per 1000 atoms: 0.48 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: 4.50 Conformation dependent library (CDL) restraints added in 1.3 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: 7.78 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: 6.60 Time building geometry restraints manager: 5.54 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: 1.910 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: 0.270 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 52.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.090 ------------------------------------------------------------------------------- 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 9482 Z= 0.099 Angle : 0.438 7.033 12926 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 Details of bonding type rmsd hydrogen bonds : bond 0.12128 ( 401) hydrogen bonds : angle 4.69309 ( 1108) metal coordination : bond 0.00146 ( 4) metal coordination : angle 0.72439 ( 1) covalent geometry : bond 0.00217 ( 9478) covalent geometry : angle 0.43825 (12925) *********************** 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 to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.450 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: 2.4538 time to fit residues: 319.4553 Evaluate side-chains 112 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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: 0.0770 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: 0.8340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.086776 restraints weight = 34026.571| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.72 r_work: 0.2859 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9482 Z= 0.126 Angle : 0.462 3.889 12926 Z= 0.245 Chirality : 0.036 0.142 1474 Planarity : 0.004 0.054 1563 Dihedral : 11.975 73.575 1630 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.37 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: 1.00 (0.26), residues: 1094 helix: 2.27 (0.25), residues: 441 sheet: -0.69 (0.50), residues: 112 loop : -0.37 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.005 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.05756 ( 401) hydrogen bonds : angle 3.95567 ( 1108) metal coordination : bond 0.00172 ( 4) metal coordination : angle 1.24900 ( 1) covalent geometry : bond 0.00286 ( 9478) covalent geometry : angle 0.46233 (12925) *********************** 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 120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.525 Fit side-chains REVERT: C 88 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7298 (mp10) outliers start: 19 outliers final: 9 residues processed: 111 average time/residue: 2.4579 time to fit residues: 293.9483 Evaluate side-chains 113 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 56 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.083552 restraints weight = 34161.479| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.71 r_work: 0.2803 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9482 Z= 0.209 Angle : 0.511 5.594 12926 Z= 0.272 Chirality : 0.038 0.148 1474 Planarity : 0.004 0.048 1563 Dihedral : 11.926 73.631 1617 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.40 % Allowed : 19.40 % 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: 0.71 (0.25), residues: 1094 helix: 1.99 (0.25), residues: 442 sheet: -1.01 (0.52), residues: 100 loop : -0.48 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.007 0.001 HIS B 174 PHE 0.015 0.001 PHE C 44 TYR 0.015 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.06297 ( 401) hydrogen bonds : angle 3.99612 ( 1108) metal coordination : bond 0.01280 ( 4) metal coordination : angle 1.95111 ( 1) covalent geometry : bond 0.00486 ( 9478) covalent geometry : angle 0.51031 (12925) *********************** 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 131 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.463 Fit side-chains REVERT: B 148 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: C 83 ARG cc_start: 0.7429 (tmm-80) cc_final: 0.7053 (tmm-80) REVERT: C 88 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: C 89 GLU cc_start: 0.7752 (mp0) cc_final: 0.7530 (mm-30) outliers start: 23 outliers final: 10 residues processed: 121 average time/residue: 2.6570 time to fit residues: 345.9842 Evaluate side-chains 111 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 113 VAL 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 18 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.084135 restraints weight = 34221.066| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.75 r_work: 0.2813 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9482 Z= 0.141 Angle : 0.473 4.412 12926 Z= 0.250 Chirality : 0.037 0.145 1474 Planarity : 0.004 0.040 1563 Dihedral : 11.826 73.591 1617 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.98 % Allowed : 19.60 % Favored : 78.42 % 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: 0.72 (0.25), residues: 1094 helix: 2.03 (0.25), residues: 442 sheet: -0.97 (0.52), residues: 100 loop : -0.50 (0.25), residues: 552 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 0.003 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.05845 ( 401) hydrogen bonds : angle 3.88515 ( 1108) metal coordination : bond 0.00591 ( 4) metal coordination : angle 1.45360 ( 1) covalent geometry : bond 0.00328 ( 9478) covalent geometry : angle 0.47315 (12925) *********************** 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 121 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.474 Fit side-chains REVERT: B 148 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: C 83 ARG cc_start: 0.7441 (tmm-80) cc_final: 0.7079 (tmm-80) REVERT: C 88 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7303 (mp10) outliers start: 19 outliers final: 10 residues processed: 112 average time/residue: 2.5144 time to fit residues: 304.2174 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.083093 restraints weight = 34623.111| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.75 r_work: 0.2797 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9482 Z= 0.175 Angle : 0.491 4.891 12926 Z= 0.261 Chirality : 0.037 0.146 1474 Planarity : 0.004 0.038 1563 Dihedral : 11.824 73.626 1617 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.88 % Allowed : 19.92 % 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: 0.64 (0.25), residues: 1094 helix: 1.94 (0.25), residues: 442 sheet: -0.94 (0.58), residues: 88 loop : -0.56 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.013 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.06029 ( 401) hydrogen bonds : angle 3.91972 ( 1108) metal coordination : bond 0.00972 ( 4) metal coordination : angle 2.35077 ( 1) covalent geometry : bond 0.00408 ( 9478) covalent geometry : angle 0.49027 (12925) *********************** 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 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.487 Fit side-chains REVERT: B 204 GLU cc_start: 0.8407 (tt0) cc_final: 0.8183 (tp30) REVERT: C 83 ARG cc_start: 0.7437 (tmm-80) cc_final: 0.7064 (tmm-80) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 2.8133 time to fit residues: 344.4500 Evaluate side-chains 112 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 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 105 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084850 restraints weight = 34517.238| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.76 r_work: 0.2824 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9482 Z= 0.112 Angle : 0.461 5.390 12926 Z= 0.242 Chirality : 0.036 0.144 1474 Planarity : 0.004 0.037 1563 Dihedral : 11.718 74.344 1617 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.56 % Allowed : 20.33 % 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: 0.77 (0.26), residues: 1094 helix: 2.08 (0.25), residues: 442 sheet: -0.89 (0.58), residues: 88 loop : -0.52 (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 A 367 PHE 0.008 0.001 PHE C 44 TYR 0.012 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.05570 ( 401) hydrogen bonds : angle 3.79380 ( 1108) metal coordination : bond 0.00228 ( 4) metal coordination : angle 1.13118 ( 1) covalent geometry : bond 0.00257 ( 9478) covalent geometry : angle 0.46096 (12925) *********************** 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 121 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 4.453 Fit side-chains REVERT: B 148 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: C 83 ARG cc_start: 0.7424 (tmm-80) cc_final: 0.7057 (tmm-80) outliers start: 15 outliers final: 11 residues processed: 112 average time/residue: 3.0054 time to fit residues: 368.7560 Evaluate side-chains 114 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 108 LEU 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 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.0060 chunk 43 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084947 restraints weight = 34444.385| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.76 r_work: 0.2843 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9482 Z= 0.100 Angle : 0.445 4.424 12926 Z= 0.233 Chirality : 0.036 0.141 1474 Planarity : 0.003 0.037 1563 Dihedral : 11.624 75.912 1617 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.36 % Allowed : 21.06 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1094 helix: 2.19 (0.25), residues: 442 sheet: -0.76 (0.58), residues: 86 loop : -0.50 (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 0.007 0.001 PHE C 44 TYR 0.012 0.001 TYR C 95 ARG 0.002 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 401) hydrogen bonds : angle 3.70336 ( 1108) metal coordination : bond 0.00182 ( 4) metal coordination : angle 1.03752 ( 1) covalent geometry : bond 0.00231 ( 9478) covalent geometry : angle 0.44483 (12925) *********************** 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 119 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 148 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: B 327 LEU cc_start: 0.8332 (tt) cc_final: 0.7945 (pp) REVERT: B 397 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8664 (p0) REVERT: C 83 ARG cc_start: 0.7410 (tmm-80) cc_final: 0.7063 (tmm-80) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 2.3173 time to fit residues: 280.6013 Evaluate side-chains 112 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 397 ASN 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 108 LEU 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 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 99 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 155 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.087106 restraints weight = 34397.301| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.76 r_work: 0.2843 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9482 Z= 0.109 Angle : 0.453 4.598 12926 Z= 0.237 Chirality : 0.036 0.140 1474 Planarity : 0.004 0.076 1563 Dihedral : 11.558 75.523 1615 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.15 % Allowed : 21.27 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1094 helix: 2.20 (0.25), residues: 442 sheet: -0.76 (0.58), residues: 86 loop : -0.49 (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 0.011 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.05379 ( 401) hydrogen bonds : angle 3.69907 ( 1108) metal coordination : bond 0.00239 ( 4) metal coordination : angle 1.16234 ( 1) covalent geometry : bond 0.00254 ( 9478) covalent geometry : angle 0.45323 (12925) *********************** 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 116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: B 148 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: C 83 ARG cc_start: 0.7431 (tmm-80) cc_final: 0.7069 (tmm-80) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 2.4049 time to fit residues: 281.4171 Evaluate side-chains 111 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER 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 103 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 155 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.083841 restraints weight = 34459.280| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.76 r_work: 0.2825 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9482 Z= 0.137 Angle : 0.464 4.025 12926 Z= 0.244 Chirality : 0.036 0.141 1474 Planarity : 0.004 0.063 1563 Dihedral : 11.600 73.968 1615 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.36 % Allowed : 20.86 % Favored : 77.79 % 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: 0.84 (0.26), residues: 1094 helix: 2.14 (0.25), residues: 442 sheet: -0.80 (0.58), residues: 86 loop : -0.50 (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 0.011 0.001 PHE C 44 TYR 0.013 0.001 TYR C 95 ARG 0.008 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.05565 ( 401) hydrogen bonds : angle 3.74460 ( 1108) metal coordination : bond 0.00568 ( 4) metal coordination : angle 1.63465 ( 1) covalent geometry : bond 0.00320 ( 9478) covalent geometry : angle 0.46397 (12925) *********************** 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 116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: B 148 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: C 83 ARG cc_start: 0.7432 (tmm-80) cc_final: 0.7056 (tmm-80) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 2.3474 time to fit residues: 271.4299 Evaluate side-chains 107 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 444 ASP Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 496 SER 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 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085777 restraints weight = 34950.656| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.74 r_work: 0.2836 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9482 Z= 0.116 Angle : 0.462 5.270 12926 Z= 0.242 Chirality : 0.036 0.141 1474 Planarity : 0.004 0.064 1563 Dihedral : 11.587 74.712 1615 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.15 % Allowed : 21.06 % Favored : 77.79 % 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: 0.87 (0.26), residues: 1094 helix: 2.18 (0.25), residues: 442 sheet: -0.80 (0.58), residues: 86 loop : -0.49 (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 0.009 0.001 PHE C 44 TYR 0.013 0.001 TYR C 95 ARG 0.009 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 401) hydrogen bonds : angle 3.72239 ( 1108) metal coordination : bond 0.00306 ( 4) metal coordination : angle 1.35219 ( 1) covalent geometry : bond 0.00273 ( 9478) covalent geometry : angle 0.46182 (12925) ********************** 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 112 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: B 117 THR cc_start: 0.8896 (m) cc_final: 0.8584 (m) REVERT: B 148 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: C 83 ARG cc_start: 0.7396 (tmm-80) cc_final: 0.7029 (tmm-80) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 2.4123 time to fit residues: 270.6954 Evaluate side-chains 113 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 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 = 0.3357 r_free = 0.3357 target = 0.114114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084825 restraints weight = 34261.032| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.73 r_work: 0.2837 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9482 Z= 0.126 Angle : 0.460 4.421 12926 Z= 0.241 Chirality : 0.036 0.141 1474 Planarity : 0.004 0.061 1563 Dihedral : 11.600 74.004 1615 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.25 % Allowed : 20.96 % Favored : 77.79 % 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: 0.85 (0.26), residues: 1094 helix: 2.15 (0.25), residues: 442 sheet: -0.86 (0.58), residues: 86 loop : -0.49 (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 0.010 0.001 PHE C 44 TYR 0.014 0.001 TYR C 95 ARG 0.008 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 401) hydrogen bonds : angle 3.73645 ( 1108) metal coordination : bond 0.00442 ( 4) metal coordination : angle 1.55152 ( 1) covalent geometry : bond 0.00296 ( 9478) covalent geometry : angle 0.46023 (12925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12978.64 seconds wall clock time: 224 minutes 54.74 seconds (13494.74 seconds total)