Starting phenix.real_space_refine on Tue Jul 29 16:09:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga9_29894/07_2025/8ga9_29894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga9_29894/07_2025/8ga9_29894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ga9_29894/07_2025/8ga9_29894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga9_29894/07_2025/8ga9_29894.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga9_29894/07_2025/8ga9_29894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga9_29894/07_2025/8ga9_29894.cif" } resolution = 3.71 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 3840 2.51 5 N 836 2.21 5 O 976 1.98 5 H 5864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "G" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Time building chain proxies: 7.51, per 1000 atoms: 0.65 Number of scatterers: 11552 At special positions: 0 Unit cell: (89.385, 88.5, 61.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 976 8.00 N 836 7.00 C 3840 6.00 H 5864 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: 3.33 Conformation dependent library (CDL) restraints added in 764.8 milliseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 4.236A pdb=" N LEU A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.534A pdb=" N GLN A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.981A pdb=" N GLU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.509A pdb=" N LEU A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.911A pdb=" N GLU A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.511A pdb=" N PHE A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.899A pdb=" N ASN A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.679A pdb=" N LYS A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.718A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 192 through 206 removed outlier: 4.122A pdb=" N GLU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.531A pdb=" N LEU C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 235 removed outlier: 3.786A pdb=" N GLU C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.476A pdb=" N LEU C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 278 through 292 removed outlier: 3.672A pdb=" N TYR C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 289 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 Processing helix chain 'C' and resid 307 through 319 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 358 through 372 removed outlier: 4.255A pdb=" N GLU E 364 " --> pdb=" O GLU E 360 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 385 removed outlier: 3.602A pdb=" N LEU E 378 " --> pdb=" O GLY E 374 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 385 " --> pdb=" O ARG E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 removed outlier: 3.535A pdb=" N GLN E 391 " --> pdb=" O HIS E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 415 removed outlier: 3.572A pdb=" N PHE E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 406 " --> pdb=" O PRO E 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 412 " --> pdb=" O PHE E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 427 Processing helix chain 'E' and resid 430 through 443 removed outlier: 3.748A pdb=" N GLN E 434 " --> pdb=" O HIS E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 removed outlier: 3.683A pdb=" N LYS E 456 " --> pdb=" O PHE E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 472 removed outlier: 4.611A pdb=" N LEU E 464 " --> pdb=" O GLY E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 485 Processing helix chain 'E' and resid 487 through 497 Processing helix chain 'G' and resid 500 through 509 Processing helix chain 'G' and resid 510 through 523 removed outlier: 3.517A pdb=" N GLN G 514 " --> pdb=" O PRO G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 538 removed outlier: 4.151A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 538 " --> pdb=" O ARG G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 551 removed outlier: 3.849A pdb=" N LEU G 544 " --> pdb=" O GLY G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 566 removed outlier: 3.610A pdb=" N GLU G 566 " --> pdb=" O GLU G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 581 removed outlier: 3.736A pdb=" N GLU G 576 " --> pdb=" O LYS G 572 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 578 " --> pdb=" O PHE G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 593 Processing helix chain 'G' and resid 596 through 609 Processing helix chain 'G' and resid 610 through 624 removed outlier: 3.670A pdb=" N LYS G 622 " --> pdb=" O PHE G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 637 Processing helix chain 'G' and resid 639 through 651 Processing helix chain 'G' and resid 653 through 662 380 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 5856 1.13 - 1.31: 988 1.31 - 1.48: 2108 1.48 - 1.66: 2688 1.66 - 1.83: 64 Bond restraints: 11704 Sorted by residual: bond pdb=" CD2 PHE G 531 " pdb=" HD2 PHE G 531 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 HIS G 553 " pdb=" HE2 HIS G 553 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL E 497 " pdb=" H VAL E 497 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 HIS E 387 " pdb=" HE1 HIS E 387 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLN C 225 " pdb=" H GLN C 225 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 11699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 17454 2.61 - 5.22: 3284 5.22 - 7.83: 613 7.83 - 10.44: 54 10.44 - 13.05: 7 Bond angle restraints: 21412 Sorted by residual: angle pdb=" CA ASN E 358 " pdb=" CB ASN E 358 " pdb=" CG ASN E 358 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" C MET E 343 " pdb=" N PRO E 344 " pdb=" CA PRO E 344 " ideal model delta sigma weight residual 119.66 123.82 -4.16 7.30e-01 1.88e+00 3.25e+01 angle pdb=" CB HIS C 264 " pdb=" CG HIS C 264 " pdb=" CD2 HIS C 264 " ideal model delta sigma weight residual 131.20 124.15 7.05 1.30e+00 5.92e-01 2.94e+01 angle pdb=" CA PHE C 200 " pdb=" CB PHE C 200 " pdb=" CG PHE C 200 " ideal model delta sigma weight residual 113.80 108.44 5.36 1.00e+00 1.00e+00 2.88e+01 angle pdb=" C ASN E 401 " pdb=" N PRO E 402 " pdb=" CA PRO E 402 " ideal model delta sigma weight residual 119.82 125.06 -5.24 9.80e-01 1.04e+00 2.86e+01 ... (remaining 21407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5032 17.71 - 35.41: 283 35.41 - 53.11: 93 53.11 - 70.82: 43 70.82 - 88.52: 9 Dihedral angle restraints: 5460 sinusoidal: 2984 harmonic: 2476 Sorted by residual: dihedral pdb=" CA PHE A 77 " pdb=" C PHE A 77 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG E 457 " pdb=" C ARG E 457 " pdb=" N CYS E 458 " pdb=" CA CYS E 458 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASN G 567 " pdb=" C ASN G 567 " pdb=" N PRO G 568 " pdb=" CA PRO G 568 " ideal model delta harmonic sigma weight residual 180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 527 0.087 - 0.175: 249 0.175 - 0.262: 51 0.262 - 0.349: 15 0.349 - 0.436: 2 Chirality restraints: 844 Sorted by residual: chirality pdb=" CA PHE A 77 " pdb=" N PHE A 77 " pdb=" C PHE A 77 " pdb=" CB PHE A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA PRO E 431 " pdb=" N PRO E 431 " pdb=" C PRO E 431 " pdb=" CB PRO E 431 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA MET C 167 " pdb=" N MET C 167 " pdb=" C MET C 167 " pdb=" CB MET C 167 " both_signs ideal model delta sigma weight residual False 2.57 2.24 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 841 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 155 " 0.096 2.00e-02 2.50e+03 8.84e-02 1.17e+02 pdb=" CG ASN A 155 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 155 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN A 155 " -0.076 2.00e-02 2.50e+03 pdb="HD21 ASN A 155 " -0.070 2.00e-02 2.50e+03 pdb="HD22 ASN A 155 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 550 " -0.129 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG TYR G 550 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR G 550 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR G 550 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR G 550 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR G 550 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR G 550 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR G 550 " -0.118 2.00e-02 2.50e+03 pdb=" HD1 TYR G 550 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR G 550 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR G 550 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR G 550 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 25 " -0.088 2.00e-02 2.50e+03 8.19e-02 1.01e+02 pdb=" CG ASN A 25 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 25 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 25 " 0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 25 " 0.060 2.00e-02 2.50e+03 pdb="HD22 ASN A 25 " -0.137 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 92 1.91 - 2.59: 10184 2.59 - 3.26: 35690 3.26 - 3.93: 44115 3.93 - 4.60: 65969 Nonbonded interactions: 156050 Sorted by model distance: nonbonded pdb="HD12 LEU C 260 " pdb="HD11 LEU C 263 " model vdw 1.242 2.440 nonbonded pdb=" HE2 PHE A 116 " pdb="HD23 LEU A 161 " model vdw 1.568 2.270 nonbonded pdb="HD22 LEU A 106 " pdb="HD21 LEU A 148 " model vdw 1.614 2.440 nonbonded pdb=" O GLN A 102 " pdb="HD13 LEU A 106 " model vdw 1.636 2.620 nonbonded pdb=" OE2 GLU A 78 " pdb=" HH TYR A 122 " model vdw 1.652 2.450 ... (remaining 156045 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 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: 0.190 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 30.340 Find NCS groups from input model: 0.310 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.014 0.051 5840 Z= 0.819 Angle : 1.814 8.192 7864 Z= 1.212 Chirality : 0.103 0.436 844 Planarity : 0.015 0.100 996 Dihedral : 13.583 88.525 2304 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.27), residues: 652 helix: -1.92 (0.16), residues: 584 sheet: None (None), residues: 0 loop : 1.59 (0.83), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS G 596 PHE 0.100 0.015 PHE E 452 TYR 0.115 0.023 TYR G 550 ARG 0.015 0.003 ARG G 547 Details of bonding type rmsd hydrogen bonds : bond 0.20216 ( 380) hydrogen bonds : angle 7.82187 ( 1140) covalent geometry : bond 0.01449 ( 5840) covalent geometry : angle 1.81358 ( 7864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6636 (ttpt) REVERT: C 282 PHE cc_start: 0.8393 (t80) cc_final: 0.8058 (t80) REVERT: C 312 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7999 (mppt) REVERT: E 432 MET cc_start: 0.7676 (mpp) cc_final: 0.7461 (mpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3867 time to fit residues: 93.8103 Evaluate side-chains 142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN G 524 ASN G 587 GLN G 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.182340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.160848 restraints weight = 23489.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.167551 restraints weight = 11000.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171822 restraints weight = 6304.499| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 5840 Z= 0.223 Angle : 0.787 8.513 7864 Z= 0.404 Chirality : 0.041 0.162 844 Planarity : 0.005 0.041 996 Dihedral : 5.893 28.827 708 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.74 % Allowed : 9.02 % Favored : 89.24 % 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: -0.95 (0.29), residues: 652 helix: -0.65 (0.18), residues: 598 sheet: None (None), residues: 0 loop : 2.23 (0.97), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 387 PHE 0.022 0.002 PHE E 452 TYR 0.014 0.002 TYR C 227 ARG 0.005 0.001 ARG G 547 Details of bonding type rmsd hydrogen bonds : bond 0.07165 ( 380) hydrogen bonds : angle 5.36912 ( 1140) covalent geometry : bond 0.00491 ( 5840) covalent geometry : angle 0.78745 ( 7864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 657 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7618 (tppt) outliers start: 11 outliers final: 8 residues processed: 149 average time/residue: 0.3733 time to fit residues: 78.7703 Evaluate side-chains 133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain G residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN C 268 GLN C 278 ASN E 444 ASN G 587 GLN G 610 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.179248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.157770 restraints weight = 23276.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164415 restraints weight = 10899.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.168645 restraints weight = 6268.461| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5840 Z= 0.190 Angle : 0.680 8.662 7864 Z= 0.346 Chirality : 0.039 0.158 844 Planarity : 0.005 0.036 996 Dihedral : 5.426 26.486 708 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.06 % Allowed : 9.81 % Favored : 88.13 % 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: -0.23 (0.30), residues: 652 helix: -0.11 (0.19), residues: 596 sheet: None (None), residues: 0 loop : 1.26 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 596 PHE 0.017 0.002 PHE E 452 TYR 0.010 0.002 TYR C 172 ARG 0.002 0.000 ARG E 457 Details of bonding type rmsd hydrogen bonds : bond 0.05700 ( 380) hydrogen bonds : angle 5.04074 ( 1140) covalent geometry : bond 0.00429 ( 5840) covalent geometry : angle 0.67993 ( 7864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.6913 (m-40) cc_final: 0.6702 (m-40) REVERT: C 211 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 270 GLU cc_start: 0.6959 (tp30) cc_final: 0.6695 (tp30) REVERT: E 424 LEU cc_start: 0.8647 (mm) cc_final: 0.8420 (mm) REVERT: G 586 GLU cc_start: 0.6071 (mp0) cc_final: 0.5760 (mp0) outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 0.2959 time to fit residues: 54.2911 Evaluate side-chains 127 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN C 255 GLN E 425 ASN G 587 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150359 restraints weight = 22919.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.157021 restraints weight = 10794.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161351 restraints weight = 6056.638| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5840 Z= 0.189 Angle : 0.640 8.212 7864 Z= 0.323 Chirality : 0.038 0.161 844 Planarity : 0.005 0.057 996 Dihedral : 5.151 25.547 708 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.37 % Allowed : 10.28 % Favored : 87.34 % 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: 0.21 (0.31), residues: 652 helix: 0.25 (0.20), residues: 598 sheet: None (None), residues: 0 loop : 0.55 (0.98), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 387 PHE 0.012 0.002 PHE A 120 TYR 0.014 0.002 TYR C 172 ARG 0.002 0.000 ARG C 291 Details of bonding type rmsd hydrogen bonds : bond 0.05097 ( 380) hydrogen bonds : angle 4.79857 ( 1140) covalent geometry : bond 0.00429 ( 5840) covalent geometry : angle 0.63978 ( 7864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.7214 (m-40) cc_final: 0.6896 (m-40) REVERT: C 211 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7606 (mm-30) REVERT: E 420 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6782 (mm-30) REVERT: E 424 LEU cc_start: 0.8525 (mm) cc_final: 0.8299 (mm) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 0.3439 time to fit residues: 61.8896 Evaluate side-chains 126 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.170224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149325 restraints weight = 23027.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155879 restraints weight = 10706.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.160130 restraints weight = 6007.027| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5840 Z= 0.205 Angle : 0.637 8.416 7864 Z= 0.323 Chirality : 0.038 0.175 844 Planarity : 0.005 0.034 996 Dihedral : 5.056 25.009 708 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.69 % Allowed : 12.34 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.31), residues: 652 helix: 0.35 (0.20), residues: 598 sheet: None (None), residues: 0 loop : 0.19 (0.98), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 387 PHE 0.014 0.002 PHE A 120 TYR 0.011 0.002 TYR E 384 ARG 0.002 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 380) hydrogen bonds : angle 4.77226 ( 1140) covalent geometry : bond 0.00467 ( 5840) covalent geometry : angle 0.63671 ( 7864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7556 (mm-30) REVERT: E 420 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6713 (mm-30) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 0.3059 time to fit residues: 55.5202 Evaluate side-chains 127 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 477 GLN G 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.169052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146497 restraints weight = 24127.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153255 restraints weight = 11735.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157609 restraints weight = 6824.330| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5840 Z= 0.195 Angle : 0.619 8.227 7864 Z= 0.313 Chirality : 0.038 0.168 844 Planarity : 0.004 0.033 996 Dihedral : 4.941 24.691 708 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.37 % Allowed : 13.45 % Favored : 84.18 % 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: 0.37 (0.31), residues: 652 helix: 0.41 (0.20), residues: 605 sheet: None (None), residues: 0 loop : -0.33 (1.05), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 387 PHE 0.013 0.002 PHE A 120 TYR 0.013 0.002 TYR A 147 ARG 0.002 0.000 ARG E 381 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 380) hydrogen bonds : angle 4.67171 ( 1140) covalent geometry : bond 0.00447 ( 5840) covalent geometry : angle 0.61904 ( 7864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7540 (mm-30) REVERT: E 420 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6553 (mm-30) outliers start: 15 outliers final: 9 residues processed: 129 average time/residue: 0.3583 time to fit residues: 65.9473 Evaluate side-chains 129 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 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 89 GLN E 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.169715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147464 restraints weight = 23970.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154194 restraints weight = 11576.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158483 restraints weight = 6658.243| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5840 Z= 0.172 Angle : 0.596 7.571 7864 Z= 0.300 Chirality : 0.037 0.157 844 Planarity : 0.004 0.034 996 Dihedral : 4.834 24.560 708 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.22 % Allowed : 14.72 % Favored : 83.07 % 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: 0.61 (0.32), residues: 652 helix: 0.58 (0.20), residues: 605 sheet: None (None), residues: 0 loop : -0.47 (1.05), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 387 PHE 0.012 0.001 PHE A 120 TYR 0.015 0.002 TYR A 147 ARG 0.002 0.001 ARG G 534 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 380) hydrogen bonds : angle 4.50106 ( 1140) covalent geometry : bond 0.00393 ( 5840) covalent geometry : angle 0.59615 ( 7864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7489 (mm-30) REVERT: E 420 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6502 (mm-30) REVERT: G 586 GLU cc_start: 0.6180 (mp0) cc_final: 0.5613 (mt-10) REVERT: G 587 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6469 (tm130) REVERT: G 591 ASN cc_start: 0.6241 (m-40) cc_final: 0.5966 (m-40) outliers start: 14 outliers final: 8 residues processed: 127 average time/residue: 0.3221 time to fit residues: 57.5993 Evaluate side-chains 131 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148819 restraints weight = 23982.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.155556 restraints weight = 11538.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.159978 restraints weight = 6657.658| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5840 Z= 0.143 Angle : 0.573 6.846 7864 Z= 0.286 Chirality : 0.036 0.140 844 Planarity : 0.004 0.038 996 Dihedral : 4.678 24.087 708 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.22 % Allowed : 15.35 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.32), residues: 652 helix: 0.76 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.74 (1.06), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 596 PHE 0.011 0.001 PHE E 366 TYR 0.013 0.001 TYR A 147 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 380) hydrogen bonds : angle 4.29240 ( 1140) covalent geometry : bond 0.00331 ( 5840) covalent geometry : angle 0.57322 ( 7864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 420 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6564 (mm-30) REVERT: G 586 GLU cc_start: 0.6174 (mp0) cc_final: 0.5591 (mt-10) REVERT: G 587 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6350 (tm130) outliers start: 14 outliers final: 8 residues processed: 135 average time/residue: 0.3028 time to fit residues: 57.0047 Evaluate side-chains 132 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 643 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.149105 restraints weight = 23626.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155885 restraints weight = 11451.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160311 restraints weight = 6591.898| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5840 Z= 0.154 Angle : 0.585 6.908 7864 Z= 0.291 Chirality : 0.036 0.145 844 Planarity : 0.004 0.038 996 Dihedral : 4.655 23.829 708 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.74 % Allowed : 15.98 % Favored : 82.28 % 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: 0.93 (0.32), residues: 652 helix: 0.83 (0.20), residues: 607 sheet: None (None), residues: 0 loop : -1.03 (1.08), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 596 PHE 0.011 0.001 PHE A 120 TYR 0.012 0.001 TYR A 147 ARG 0.001 0.000 ARG G 534 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 380) hydrogen bonds : angle 4.29323 ( 1140) covalent geometry : bond 0.00364 ( 5840) covalent geometry : angle 0.58494 ( 7864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 419 MET cc_start: 0.6641 (mmt) cc_final: 0.6217 (mmt) REVERT: E 420 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: G 586 GLU cc_start: 0.6142 (mp0) cc_final: 0.5656 (mt-10) REVERT: G 587 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6519 (tm130) outliers start: 11 outliers final: 8 residues processed: 131 average time/residue: 0.2991 time to fit residues: 55.5215 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.169993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147844 restraints weight = 23784.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154610 restraints weight = 11603.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.158935 restraints weight = 6679.599| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5840 Z= 0.155 Angle : 0.592 6.940 7864 Z= 0.295 Chirality : 0.037 0.146 844 Planarity : 0.004 0.038 996 Dihedral : 4.601 23.905 708 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.58 % Allowed : 15.66 % Favored : 82.75 % 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: 1.05 (0.32), residues: 652 helix: 0.90 (0.20), residues: 607 sheet: None (None), residues: 0 loop : -1.05 (1.09), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 596 PHE 0.011 0.001 PHE A 120 TYR 0.010 0.001 TYR A 147 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 380) hydrogen bonds : angle 4.27450 ( 1140) covalent geometry : bond 0.00362 ( 5840) covalent geometry : angle 0.59170 ( 7864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.6939 (pm20) cc_final: 0.6227 (tp30) REVERT: E 419 MET cc_start: 0.6589 (mmt) cc_final: 0.6197 (mmt) REVERT: E 420 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6590 (mm-30) REVERT: G 586 GLU cc_start: 0.6252 (mp0) cc_final: 0.5728 (mt-10) REVERT: G 587 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6697 (tm130) outliers start: 10 outliers final: 7 residues processed: 130 average time/residue: 0.2960 time to fit residues: 55.0489 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 17 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148784 restraints weight = 23777.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.155586 restraints weight = 11518.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.159985 restraints weight = 6646.639| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5840 Z= 0.139 Angle : 0.579 6.451 7864 Z= 0.288 Chirality : 0.036 0.136 844 Planarity : 0.004 0.037 996 Dihedral : 4.518 24.084 708 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.58 % Allowed : 15.66 % Favored : 82.75 % 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: 1.23 (0.32), residues: 652 helix: 1.02 (0.20), residues: 607 sheet: None (None), residues: 0 loop : -1.01 (1.11), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 596 PHE 0.011 0.001 PHE G 571 TYR 0.013 0.001 TYR A 79 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 380) hydrogen bonds : angle 4.16454 ( 1140) covalent geometry : bond 0.00325 ( 5840) covalent geometry : angle 0.57859 ( 7864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4295.30 seconds wall clock time: 75 minutes 31.83 seconds (4531.83 seconds total)