Starting phenix.real_space_refine on Wed Feb 4 18:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7q_65730/02_2026/9w7q_65730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7q_65730/02_2026/9w7q_65730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w7q_65730/02_2026/9w7q_65730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7q_65730/02_2026/9w7q_65730.map" model { file = "/net/cci-nas-00/data/ceres_data/9w7q_65730/02_2026/9w7q_65730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7q_65730/02_2026/9w7q_65730.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.006 sd= 0.044 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 P 135 5.49 5 S 19 5.16 5 C 7195 2.51 5 N 2128 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12105 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9201 Classifications: {'peptide': 1129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1098} Chain breaks: 2 Chain: "B" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 618 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1981 Classifications: {'RNA': 93} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 37} Link IDs: {'rna2p': 11, 'rna3p': 81} Time building chain proxies: 2.16, per 1000 atoms: 0.18 Number of scatterers: 12105 At special positions: 0 Unit cell: (134.75, 104.566, 144.452, 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 19 16.00 P 135 15.00 O 2628 8.00 N 2128 7.00 C 7195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.93 Conformation dependent library (CDL) restraints added in 376.3 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 56.2% alpha, 8.0% beta 52 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.769A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.781A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.546A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.037A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.528A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 removed outlier: 4.369A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 307 removed outlier: 3.649A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.725A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.223A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.063A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.580A pdb=" N GLN A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.120A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.538A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.627A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.665A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.071A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 4.437A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.517A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.596A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1317 removed outlier: 3.604A pdb=" N ASN A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1317' Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.768A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 4.250A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 7 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 760 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.475A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 942 through 943 removed outlier: 4.706A pdb=" N LYS A 942 " --> pdb=" O ILE A 950 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.625A pdb=" N ALA A1147 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.709A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 260 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2639 1.33 - 1.45: 3274 1.45 - 1.57: 6400 1.57 - 1.69: 270 1.69 - 1.81: 36 Bond restraints: 12619 Sorted by residual: bond pdb=" CB PRO A 250 " pdb=" CG PRO A 250 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.29e+00 bond pdb=" C4' DA B 24 " pdb=" C3' DA B 24 " ideal model delta sigma weight residual 1.523 1.501 0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" CA TYR A 568 " pdb=" C TYR A 568 " ideal model delta sigma weight residual 1.525 1.514 0.011 1.02e-02 9.61e+03 1.11e+00 bond pdb=" C3' DT B 10 " pdb=" C2' DT B 10 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CB TRP A 464 " pdb=" CG TRP A 464 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 ... (remaining 12614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 16925 1.40 - 2.79: 637 2.79 - 4.19: 64 4.19 - 5.58: 13 5.58 - 6.98: 1 Bond angle restraints: 17640 Sorted by residual: angle pdb=" CA VAL A1280 " pdb=" C VAL A1280 " pdb=" N ILE A1281 " ideal model delta sigma weight residual 116.60 120.87 -4.27 1.45e+00 4.76e-01 8.67e+00 angle pdb=" N ASP A 585 " pdb=" CA ASP A 585 " pdb=" CB ASP A 585 " ideal model delta sigma weight residual 113.65 110.03 3.62 1.47e+00 4.63e-01 6.05e+00 angle pdb=" C PHE A1327 " pdb=" CA PHE A1327 " pdb=" CB PHE A1327 " ideal model delta sigma weight residual 110.42 115.30 -4.88 1.99e+00 2.53e-01 6.00e+00 angle pdb=" C4' DC C 10 " pdb=" O4' DC C 10 " pdb=" C1' DC C 10 " ideal model delta sigma weight residual 109.70 106.06 3.64 1.50e+00 4.44e-01 5.90e+00 angle pdb=" N VAL A1280 " pdb=" CA VAL A1280 " pdb=" C VAL A1280 " ideal model delta sigma weight residual 109.34 114.30 -4.96 2.08e+00 2.31e-01 5.70e+00 ... (remaining 17635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6750 17.25 - 34.50: 538 34.50 - 51.75: 192 51.75 - 69.00: 141 69.00 - 86.25: 25 Dihedral angle restraints: 7646 sinusoidal: 4329 harmonic: 3317 Sorted by residual: dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N SER A 87 " pdb=" CA SER A 87 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR A1201 " pdb=" C TYR A1201 " pdb=" N SER A1202 " pdb=" CA SER A1202 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" N ASP A 182 " pdb=" CA ASP A 182 " ideal model delta harmonic sigma weight residual 180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 7643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1337 0.029 - 0.057: 464 0.057 - 0.086: 153 0.086 - 0.115: 68 0.115 - 0.143: 13 Chirality restraints: 2035 Sorted by residual: chirality pdb=" C1' A D 42 " pdb=" O4' A D 42 " pdb=" C2' A D 42 " pdb=" N9 A D 42 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA PRO A1128 " pdb=" N PRO A1128 " pdb=" C PRO A1128 " pdb=" CB PRO A1128 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2032 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 42 " -0.022 2.00e-02 2.50e+03 1.01e-02 2.81e+00 pdb=" N9 A D 42 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A D 42 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A D 42 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 42 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 42 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A D 42 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 42 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A D 42 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 42 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 54 " 0.020 2.00e-02 2.50e+03 8.80e-03 2.32e+00 pdb=" N9 G D 54 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G D 54 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G D 54 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G D 54 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G D 54 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G D 54 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G D 54 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G D 54 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G D 54 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G D 54 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G D 54 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 49 " 0.019 2.00e-02 2.50e+03 8.88e-03 2.17e+00 pdb=" N9 A D 49 " -0.020 2.00e-02 2.50e+03 pdb=" C8 A D 49 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A D 49 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A D 49 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A D 49 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A D 49 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A D 49 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A D 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 49 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A D 49 " -0.002 2.00e-02 2.50e+03 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 4 2.02 - 2.74: 1168 2.74 - 3.46: 17088 3.46 - 4.18: 30430 4.18 - 4.90: 48617 Nonbonded interactions: 97307 Sorted by model distance: nonbonded pdb=" NZ LYS A 510 " pdb=" O5' A D 5 " model vdw 1.298 3.120 nonbonded pdb=" ND2 ASN A 77 " pdb=" O2 U D 59 " model vdw 1.299 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" C5 C D 18 " model vdw 1.433 3.420 nonbonded pdb=" SD MET A 495 " pdb=" C1' DA B 24 " model vdw 1.771 3.830 nonbonded pdb=" OG SER A 719 " pdb=" OE1 GLU A 722 " model vdw 2.132 3.040 ... (remaining 97302 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.004 0.057 12619 Z= 0.189 Angle : 0.610 6.978 17640 Z= 0.351 Chirality : 0.036 0.143 2035 Planarity : 0.004 0.034 1751 Dihedral : 16.621 86.247 5498 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1123 helix: 1.10 (0.22), residues: 561 sheet: 0.64 (0.54), residues: 83 loop : -0.10 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.016 0.001 TYR A1141 PHE 0.018 0.002 PHE A 164 TRP 0.020 0.002 TRP A1126 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd covalent geometry : bond 0.00386 (12619) covalent geometry : angle 0.61022 (17640) hydrogen bonds : bond 0.16616 ( 572) hydrogen bonds : angle 5.71791 ( 1541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.311 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: A 534 MET cc_start: 0.5602 (mtt) cc_final: 0.5283 (ttm) REVERT: A 621 LEU cc_start: 0.9561 (tp) cc_final: 0.9336 (tp) REVERT: A 648 MET cc_start: 0.9387 (mmm) cc_final: 0.8929 (mmm) REVERT: A 930 HIS cc_start: 0.8104 (m-70) cc_final: 0.7868 (m-70) REVERT: A 1172 SER cc_start: 0.9493 (m) cc_final: 0.8922 (p) REVERT: A 1238 LEU cc_start: 0.9563 (mt) cc_final: 0.9292 (pp) REVERT: A 1357 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7872 (mp0) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1054 time to fit residues: 29.9753 Evaluate side-chains 111 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 265 GLN ** A 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 HIS A1101 GLN A1261 GLN A1286 ASN A1305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.051652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034927 restraints weight = 84015.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036384 restraints weight = 43584.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037379 restraints weight = 29019.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037922 restraints weight = 22415.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.038391 restraints weight = 19266.934| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12619 Z= 0.264 Angle : 0.684 11.585 17640 Z= 0.366 Chirality : 0.040 0.177 2035 Planarity : 0.005 0.053 1751 Dihedral : 19.143 87.966 3122 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 2.08 % Allowed : 8.82 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1123 helix: 0.84 (0.22), residues: 561 sheet: 0.98 (0.57), residues: 81 loop : -0.12 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.015 0.002 TYR A 656 PHE 0.015 0.002 PHE A 164 TRP 0.020 0.002 TRP A 659 HIS 0.006 0.002 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00533 (12619) covalent geometry : angle 0.68390 (17640) hydrogen bonds : bond 0.05375 ( 572) hydrogen bonds : angle 5.01819 ( 1541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.359 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: A 45 LYS cc_start: 0.9682 (mtmt) cc_final: 0.9070 (mmtt) REVERT: A 71 ARG cc_start: 0.9618 (mtm180) cc_final: 0.9212 (ttm170) REVERT: A 321 MET cc_start: 0.9457 (mmp) cc_final: 0.8942 (mmm) REVERT: A 327 GLU cc_start: 0.9653 (mt-10) cc_final: 0.9435 (pp20) REVERT: A 442 LYS cc_start: 0.9741 (tttt) cc_final: 0.9434 (ttpp) REVERT: A 492 ILE cc_start: 0.9845 (mm) cc_final: 0.9632 (tt) REVERT: A 516 GLU cc_start: 0.9230 (mt-10) cc_final: 0.9013 (mt-10) REVERT: A 534 MET cc_start: 0.6958 (mtt) cc_final: 0.6284 (ttm) REVERT: A 648 MET cc_start: 0.9680 (mmm) cc_final: 0.9098 (mmm) REVERT: A 734 LYS cc_start: 0.9040 (mttt) cc_final: 0.8784 (mttp) REVERT: A 751 MET cc_start: 0.9460 (tpp) cc_final: 0.9172 (ttm) REVERT: A 930 HIS cc_start: 0.8711 (m-70) cc_final: 0.8448 (m90) REVERT: A 1142 SER cc_start: 0.9805 (m) cc_final: 0.9527 (p) REVERT: A 1213 MET cc_start: 0.9428 (ttp) cc_final: 0.9130 (ttm) REVERT: A 1219 GLU cc_start: 0.9247 (tp30) cc_final: 0.9043 (tp30) REVERT: A 1286 ASN cc_start: 0.9551 (OUTLIER) cc_final: 0.9265 (p0) REVERT: A 1317 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8815 (m110) REVERT: A 1357 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8608 (tp30) outliers start: 21 outliers final: 8 residues processed: 122 average time/residue: 0.0943 time to fit residues: 16.6525 Evaluate side-chains 96 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1317 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 91 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 94 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 HIS A1350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.052797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035967 restraints weight = 82021.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037466 restraints weight = 41716.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038488 restraints weight = 27508.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.039149 restraints weight = 21102.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.039499 restraints weight = 17884.552| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12619 Z= 0.159 Angle : 0.575 11.065 17640 Z= 0.306 Chirality : 0.037 0.184 2035 Planarity : 0.004 0.049 1751 Dihedral : 18.906 89.820 3122 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.88 % Allowed : 9.32 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1123 helix: 1.14 (0.22), residues: 562 sheet: 1.09 (0.57), residues: 82 loop : -0.18 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 71 TYR 0.013 0.001 TYR A 656 PHE 0.013 0.001 PHE A 478 TRP 0.008 0.001 TRP A 659 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00328 (12619) covalent geometry : angle 0.57492 (17640) hydrogen bonds : bond 0.04177 ( 572) hydrogen bonds : angle 4.59749 ( 1541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.386 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: A 4 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8452 (tmtt) REVERT: A 45 LYS cc_start: 0.9622 (mtmt) cc_final: 0.9105 (ttpp) REVERT: A 71 ARG cc_start: 0.9615 (mtm180) cc_final: 0.9273 (mtp85) REVERT: A 101 LEU cc_start: 0.9484 (tt) cc_final: 0.8793 (mt) REVERT: A 321 MET cc_start: 0.9435 (mmp) cc_final: 0.9014 (mmm) REVERT: A 327 GLU cc_start: 0.9650 (mt-10) cc_final: 0.9445 (pp20) REVERT: A 332 LEU cc_start: 0.9394 (tp) cc_final: 0.8632 (pp) REVERT: A 442 LYS cc_start: 0.9723 (tttt) cc_final: 0.9227 (tppt) REVERT: A 492 ILE cc_start: 0.9793 (mm) cc_final: 0.9551 (tt) REVERT: A 534 MET cc_start: 0.7201 (mtt) cc_final: 0.6277 (ttm) REVERT: A 564 LEU cc_start: 0.9581 (tt) cc_final: 0.9366 (pp) REVERT: A 648 MET cc_start: 0.9708 (mmm) cc_final: 0.9156 (mmm) REVERT: A 751 MET cc_start: 0.9406 (tpp) cc_final: 0.9121 (ttp) REVERT: A 1142 SER cc_start: 0.9804 (m) cc_final: 0.9566 (p) REVERT: A 1213 MET cc_start: 0.9358 (ttp) cc_final: 0.9074 (ttm) REVERT: A 1219 GLU cc_start: 0.9257 (tp30) cc_final: 0.8873 (tp30) REVERT: A 1286 ASN cc_start: 0.9574 (OUTLIER) cc_final: 0.9236 (p0) REVERT: A 1357 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8700 (tp30) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 0.0905 time to fit residues: 13.9388 Evaluate side-chains 93 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1286 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 511 HIS ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.034635 restraints weight = 85250.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036155 restraints weight = 42989.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.037092 restraints weight = 28236.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.037707 restraints weight = 21849.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.038121 restraints weight = 18553.377| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12619 Z= 0.218 Angle : 0.610 14.558 17640 Z= 0.324 Chirality : 0.038 0.142 2035 Planarity : 0.004 0.054 1751 Dihedral : 18.964 90.686 3122 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 2.08 % Allowed : 10.21 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1123 helix: 1.05 (0.22), residues: 570 sheet: 0.54 (0.60), residues: 74 loop : -0.17 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 557 TYR 0.011 0.001 TYR A 430 PHE 0.012 0.002 PHE A 352 TRP 0.016 0.002 TRP A 659 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00438 (12619) covalent geometry : angle 0.60985 (17640) hydrogen bonds : bond 0.04652 ( 572) hydrogen bonds : angle 4.64081 ( 1541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.351 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: A 4 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8456 (tmtt) REVERT: A 45 LYS cc_start: 0.9608 (mtmt) cc_final: 0.9075 (ttpt) REVERT: A 60 GLU cc_start: 0.9510 (pm20) cc_final: 0.9248 (pm20) REVERT: A 321 MET cc_start: 0.9405 (mmp) cc_final: 0.9020 (mmm) REVERT: A 442 LYS cc_start: 0.9742 (tttt) cc_final: 0.9507 (mmtm) REVERT: A 534 MET cc_start: 0.7207 (mtt) cc_final: 0.6277 (ttm) REVERT: A 633 GLU cc_start: 0.9549 (OUTLIER) cc_final: 0.9303 (pt0) REVERT: A 648 MET cc_start: 0.9690 (mmm) cc_final: 0.9087 (mmm) REVERT: A 751 MET cc_start: 0.9373 (tpp) cc_final: 0.9004 (mtp) REVERT: A 1213 MET cc_start: 0.9343 (ttp) cc_final: 0.9032 (ttm) REVERT: A 1219 GLU cc_start: 0.9213 (tp30) cc_final: 0.8874 (tp30) REVERT: A 1286 ASN cc_start: 0.9632 (m110) cc_final: 0.9331 (p0) REVERT: A 1326 TYR cc_start: 0.9038 (t80) cc_final: 0.8087 (t80) REVERT: A 1357 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8674 (tp30) outliers start: 21 outliers final: 14 residues processed: 98 average time/residue: 0.0775 time to fit residues: 11.9150 Evaluate side-chains 92 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 40.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.050188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.033861 restraints weight = 86633.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035316 restraints weight = 43993.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036304 restraints weight = 29127.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036869 restraints weight = 22358.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037292 restraints weight = 19128.355| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12619 Z= 0.204 Angle : 0.579 12.022 17640 Z= 0.312 Chirality : 0.037 0.150 2035 Planarity : 0.004 0.053 1751 Dihedral : 18.910 92.547 3122 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 1.98 % Allowed : 11.89 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1123 helix: 1.03 (0.21), residues: 573 sheet: -0.19 (0.58), residues: 87 loop : -0.25 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 324 TYR 0.009 0.001 TYR A1141 PHE 0.012 0.001 PHE A1204 TRP 0.013 0.001 TRP A 659 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00408 (12619) covalent geometry : angle 0.57935 (17640) hydrogen bonds : bond 0.04368 ( 572) hydrogen bonds : angle 4.54710 ( 1541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9113 (ttpt) REVERT: A 60 GLU cc_start: 0.9539 (pm20) cc_final: 0.9151 (pm20) REVERT: A 332 LEU cc_start: 0.9441 (tp) cc_final: 0.8668 (pp) REVERT: A 442 LYS cc_start: 0.9730 (tttt) cc_final: 0.9440 (mmmm) REVERT: A 534 MET cc_start: 0.7336 (mtt) cc_final: 0.6317 (ttm) REVERT: A 633 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9310 (pp20) REVERT: A 648 MET cc_start: 0.9667 (mmm) cc_final: 0.9054 (mmm) REVERT: A 751 MET cc_start: 0.9341 (tpp) cc_final: 0.8963 (mtp) REVERT: A 1089 MET cc_start: 0.8829 (mmt) cc_final: 0.8423 (mmt) REVERT: A 1169 MET cc_start: 0.9326 (ttp) cc_final: 0.7928 (tmm) REVERT: A 1213 MET cc_start: 0.9314 (ttp) cc_final: 0.8972 (ttm) REVERT: A 1357 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8614 (tp30) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 0.0867 time to fit residues: 12.5864 Evaluate side-chains 85 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 95 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.049298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.033379 restraints weight = 88006.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.034799 restraints weight = 44411.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035774 restraints weight = 29308.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.036402 restraints weight = 22372.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.036730 restraints weight = 18927.115| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12619 Z= 0.231 Angle : 0.619 11.865 17640 Z= 0.330 Chirality : 0.038 0.137 2035 Planarity : 0.004 0.056 1751 Dihedral : 18.949 94.088 3122 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 2.08 % Allowed : 13.38 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1123 helix: 0.83 (0.21), residues: 575 sheet: -0.34 (0.58), residues: 87 loop : -0.38 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 557 TYR 0.009 0.001 TYR A1187 PHE 0.013 0.002 PHE A 352 TRP 0.015 0.002 TRP A 659 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00463 (12619) covalent geometry : angle 0.61893 (17640) hydrogen bonds : bond 0.04747 ( 572) hydrogen bonds : angle 4.58301 ( 1541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.401 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: A 60 GLU cc_start: 0.9577 (pm20) cc_final: 0.9133 (pm20) REVERT: A 101 LEU cc_start: 0.9383 (tt) cc_final: 0.8534 (mt) REVERT: A 442 LYS cc_start: 0.9736 (tttt) cc_final: 0.9469 (mmmm) REVERT: A 534 MET cc_start: 0.7617 (mtt) cc_final: 0.6615 (ttm) REVERT: A 633 GLU cc_start: 0.9552 (OUTLIER) cc_final: 0.9348 (pp20) REVERT: A 648 MET cc_start: 0.9675 (mmm) cc_final: 0.9059 (mmm) REVERT: A 751 MET cc_start: 0.9325 (tpp) cc_final: 0.8928 (ttt) REVERT: A 1089 MET cc_start: 0.8873 (mmt) cc_final: 0.8235 (tpp) REVERT: A 1169 MET cc_start: 0.9366 (ttp) cc_final: 0.7980 (tmm) REVERT: A 1213 MET cc_start: 0.9310 (ttp) cc_final: 0.9006 (ttm) REVERT: A 1357 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8785 (tp30) outliers start: 21 outliers final: 16 residues processed: 90 average time/residue: 0.0720 time to fit residues: 10.5781 Evaluate side-chains 86 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.033839 restraints weight = 86612.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035332 restraints weight = 43665.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036308 restraints weight = 28626.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036944 restraints weight = 21871.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.037281 restraints weight = 18433.711| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12619 Z= 0.175 Angle : 0.592 15.135 17640 Z= 0.308 Chirality : 0.037 0.202 2035 Planarity : 0.004 0.054 1751 Dihedral : 18.871 95.531 3122 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 2.18 % Allowed : 13.58 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1123 helix: 0.98 (0.21), residues: 577 sheet: -0.23 (0.58), residues: 87 loop : -0.39 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.008 0.001 TYR A1141 PHE 0.013 0.001 PHE A1204 TRP 0.011 0.001 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00356 (12619) covalent geometry : angle 0.59186 (17640) hydrogen bonds : bond 0.04148 ( 572) hydrogen bonds : angle 4.45596 ( 1541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9561 (pm20) cc_final: 0.9026 (pm20) REVERT: A 90 MET cc_start: 0.8945 (tpp) cc_final: 0.8465 (tpp) REVERT: A 332 LEU cc_start: 0.9426 (tp) cc_final: 0.8657 (pp) REVERT: A 442 LYS cc_start: 0.9708 (tttt) cc_final: 0.9434 (mmmm) REVERT: A 534 MET cc_start: 0.7711 (mtt) cc_final: 0.6815 (ttm) REVERT: A 633 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.9310 (pp20) REVERT: A 648 MET cc_start: 0.9668 (mmm) cc_final: 0.8999 (mmm) REVERT: A 751 MET cc_start: 0.9357 (tpp) cc_final: 0.8958 (ttt) REVERT: A 1089 MET cc_start: 0.8819 (mmt) cc_final: 0.8043 (tpp) REVERT: A 1169 MET cc_start: 0.9357 (ttp) cc_final: 0.8033 (tmm) REVERT: A 1357 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8150 (mp0) outliers start: 22 outliers final: 15 residues processed: 92 average time/residue: 0.0803 time to fit residues: 11.5540 Evaluate side-chains 85 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.034022 restraints weight = 86482.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.035507 restraints weight = 43701.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.036484 restraints weight = 28572.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037059 restraints weight = 21827.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037519 restraints weight = 18511.650| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12619 Z= 0.159 Angle : 0.594 14.081 17640 Z= 0.305 Chirality : 0.037 0.245 2035 Planarity : 0.003 0.053 1751 Dihedral : 18.825 96.020 3122 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.68 % Allowed : 13.88 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.25), residues: 1123 helix: 1.05 (0.22), residues: 576 sheet: 0.03 (0.58), residues: 85 loop : -0.38 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.008 0.001 TYR A 155 PHE 0.013 0.001 PHE A1204 TRP 0.010 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00326 (12619) covalent geometry : angle 0.59358 (17640) hydrogen bonds : bond 0.04017 ( 572) hydrogen bonds : angle 4.41217 ( 1541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9561 (pm20) cc_final: 0.8978 (pm20) REVERT: A 90 MET cc_start: 0.8959 (tpp) cc_final: 0.8494 (tpp) REVERT: A 332 LEU cc_start: 0.9418 (tp) cc_final: 0.8649 (pp) REVERT: A 534 MET cc_start: 0.7740 (mtt) cc_final: 0.6862 (ttm) REVERT: A 633 GLU cc_start: 0.9529 (OUTLIER) cc_final: 0.9323 (pp20) REVERT: A 648 MET cc_start: 0.9663 (mmm) cc_final: 0.8998 (mmm) REVERT: A 751 MET cc_start: 0.9361 (tpp) cc_final: 0.8932 (ttt) REVERT: A 763 MET cc_start: 0.1858 (ttt) cc_final: 0.1604 (ttm) REVERT: A 1089 MET cc_start: 0.8823 (mmt) cc_final: 0.8056 (tpp) REVERT: A 1169 MET cc_start: 0.9338 (ttp) cc_final: 0.8034 (tmm) REVERT: A 1357 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8161 (mp0) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.0820 time to fit residues: 11.3922 Evaluate side-chains 84 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN A 754 HIS A 758 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.032662 restraints weight = 89238.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.034031 restraints weight = 45186.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034966 restraints weight = 29928.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035555 restraints weight = 23016.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035871 restraints weight = 19532.023| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12619 Z= 0.275 Angle : 0.681 12.312 17640 Z= 0.360 Chirality : 0.040 0.193 2035 Planarity : 0.004 0.055 1751 Dihedral : 19.033 96.314 3122 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 1.88 % Allowed : 14.17 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1123 helix: 0.66 (0.21), residues: 574 sheet: 0.97 (0.60), residues: 73 loop : -0.59 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 340 TYR 0.011 0.002 TYR A1187 PHE 0.016 0.002 PHE A 352 TRP 0.020 0.002 TRP A 659 HIS 0.007 0.002 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00546 (12619) covalent geometry : angle 0.68109 (17640) hydrogen bonds : bond 0.05150 ( 572) hydrogen bonds : angle 4.78094 ( 1541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9551 (pm20) cc_final: 0.9000 (pm20) REVERT: A 534 MET cc_start: 0.7826 (mtt) cc_final: 0.6881 (ttm) REVERT: A 633 GLU cc_start: 0.9541 (OUTLIER) cc_final: 0.9333 (pp20) REVERT: A 648 MET cc_start: 0.9667 (mmm) cc_final: 0.8984 (mmm) REVERT: A 751 MET cc_start: 0.9370 (tpp) cc_final: 0.9122 (mtp) REVERT: A 763 MET cc_start: 0.2090 (ttt) cc_final: 0.1820 (ttm) REVERT: A 1089 MET cc_start: 0.8776 (mmt) cc_final: 0.8092 (tpp) REVERT: A 1213 MET cc_start: 0.8781 (tpt) cc_final: 0.8564 (tpt) REVERT: A 1357 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8809 (tm-30) outliers start: 19 outliers final: 16 residues processed: 85 average time/residue: 0.0778 time to fit residues: 10.9205 Evaluate side-chains 89 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 0.0270 chunk 85 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.051365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035291 restraints weight = 83487.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036769 restraints weight = 42168.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.037772 restraints weight = 27614.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.038324 restraints weight = 20959.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038813 restraints weight = 17796.034| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12619 Z= 0.119 Angle : 0.618 15.037 17640 Z= 0.309 Chirality : 0.037 0.258 2035 Planarity : 0.003 0.051 1751 Dihedral : 18.760 99.116 3122 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 0.99 % Allowed : 15.06 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1123 helix: 1.01 (0.22), residues: 576 sheet: 0.38 (0.60), residues: 79 loop : -0.37 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.013 0.001 TYR A 155 PHE 0.011 0.001 PHE A1204 TRP 0.011 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00255 (12619) covalent geometry : angle 0.61832 (17640) hydrogen bonds : bond 0.03684 ( 572) hydrogen bonds : angle 4.33966 ( 1541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9523 (pm20) cc_final: 0.8984 (pm20) REVERT: A 332 LEU cc_start: 0.9257 (tp) cc_final: 0.8521 (pp) REVERT: A 441 GLU cc_start: 0.9542 (pt0) cc_final: 0.9013 (pp20) REVERT: A 534 MET cc_start: 0.8045 (mtt) cc_final: 0.7285 (ttm) REVERT: A 633 GLU cc_start: 0.9523 (tm-30) cc_final: 0.9315 (pp20) REVERT: A 648 MET cc_start: 0.9684 (mmm) cc_final: 0.9051 (mmm) REVERT: A 751 MET cc_start: 0.9382 (tpp) cc_final: 0.8919 (ttt) REVERT: A 763 MET cc_start: 0.2023 (ttt) cc_final: 0.1734 (ttm) REVERT: A 1089 MET cc_start: 0.8761 (mmt) cc_final: 0.8234 (mmp) REVERT: A 1213 MET cc_start: 0.8639 (tpt) cc_final: 0.8401 (tpt) REVERT: A 1349 HIS cc_start: 0.9536 (m-70) cc_final: 0.9077 (m90) REVERT: A 1357 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8092 (mp0) outliers start: 10 outliers final: 7 residues processed: 88 average time/residue: 0.0762 time to fit residues: 10.9468 Evaluate side-chains 82 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 91 optimal weight: 0.0030 chunk 121 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 3.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.034075 restraints weight = 85515.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035532 restraints weight = 43106.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036497 restraints weight = 28137.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037055 restraints weight = 21418.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.037524 restraints weight = 18129.252| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12619 Z= 0.156 Angle : 0.613 15.141 17640 Z= 0.312 Chirality : 0.037 0.238 2035 Planarity : 0.003 0.053 1751 Dihedral : 18.788 98.102 3122 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.09 % Allowed : 15.26 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1123 helix: 1.07 (0.22), residues: 575 sheet: 0.12 (0.58), residues: 85 loop : -0.34 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.009 0.001 TYR A 155 PHE 0.016 0.001 PHE A1204 TRP 0.011 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00323 (12619) covalent geometry : angle 0.61333 (17640) hydrogen bonds : bond 0.03979 ( 572) hydrogen bonds : angle 4.37168 ( 1541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.77 seconds wall clock time: 34 minutes 59.56 seconds (2099.56 seconds total)