Starting phenix.real_space_refine on Fri Sep 11 20:24:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0x_0583/09_2026/6o0x_0583.map" } resolution = 3.28 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= -0.001 sd= 0.043 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 149 5.49 5 S 13 5.16 5 C 6671 2.51 5 N 2005 2.21 5 O 2419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11257 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8098 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1112, 8098 Classifications: {'peptide': 1112} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 29, 'TRANS': 1082} Chain breaks: 5 Unresolved non-hydrogen bonds: 1001 Unresolved non-hydrogen angles: 1217 Unresolved non-hydrogen dihedrals: 802 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'ASP:plan': 40, 'GLU:plan': 62, 'ASN:plan1': 19, 'GLN:plan1': 15, 'PHE:plan': 5, 'ARG:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 568 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2104 Classifications: {'RNAv2': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "c" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 463 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 2.64, per 1000 atoms: 0.23 Number of scatterers: 11257 At special positions: 0 Unit cell: (139.612, 127.072, 89.452, 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 13 16.00 P 149 15.00 O 2419 8.00 N 2005 7.00 C 6671 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: 1.01 Conformation dependent library (CDL) restraints added in 449.5 milliseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 52.2% alpha, 6.6% beta 54 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 3.928A pdb=" N LEU A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.205A 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 122 through 132 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.977A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.665A pdb=" N GLN A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.161A pdb=" N ALA A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.626A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.691A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.587A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.681A pdb=" N PHE A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.580A pdb=" N VAL A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.260A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.342A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.702A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.537A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.505A pdb=" N SER A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.667A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 626 removed outlier: 4.362A pdb=" N ILE A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 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 removed outlier: 3.874A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 750 removed outlier: 3.554A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 removed outlier: 3.511A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.861A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1000 Processing helix chain 'A' and resid 1079 through 1087 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.646A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.663A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 removed outlier: 3.797A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.721A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.475A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA5, first strand: chain 'A' and resid 1157 through 1167 removed outlier: 3.517A pdb=" N VAL A1145 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1164 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1325 387 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 1.34 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: 1993 1.33 - 1.45: 3596 1.45 - 1.57: 5877 1.57 - 1.69: 294 1.69 - 1.81: 25 Bond restraints: 11785 Sorted by residual: bond pdb=" C1' DC c 20 " pdb=" N1 DC c 20 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" C3' DT D 37 " pdb=" C2' DT D 37 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.84e+00 bond pdb=" C1' DT c 25 " pdb=" N1 DT c 25 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.42e+00 bond pdb=" C1' DT c 21 " pdb=" N1 DT c 21 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.08e+00 bond pdb=" C3' DC c 30 " pdb=" C2' DC c 30 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.70e+00 ... (remaining 11780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 16350 2.65 - 5.30: 315 5.30 - 7.95: 24 7.95 - 10.61: 3 10.61 - 13.26: 2 Bond angle restraints: 16694 Sorted by residual: angle pdb=" CA LYS A1334 " pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " ideal model delta sigma weight residual 114.10 127.36 -13.26 2.00e+00 2.50e-01 4.39e+01 angle pdb=" C3' A B 8 " pdb=" O3' A B 8 " pdb=" P A B 9 " ideal model delta sigma weight residual 119.70 126.08 -6.38 1.20e+00 6.94e-01 2.83e+01 angle pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " pdb=" CD LYS A1334 " ideal model delta sigma weight residual 111.30 123.42 -12.12 2.30e+00 1.89e-01 2.78e+01 angle pdb=" O4' DC c 17 " pdb=" C4' DC c 17 " pdb=" C3' DC c 17 " ideal model delta sigma weight residual 106.00 103.12 2.88 6.00e-01 2.78e+00 2.31e+01 angle pdb=" O4' DT c 23 " pdb=" C4' DT c 23 " pdb=" C3' DT c 23 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 ... (remaining 16689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6259 35.97 - 71.95: 373 71.95 - 107.92: 6 107.92 - 143.89: 0 143.89 - 179.86: 3 Dihedral angle restraints: 6641 sinusoidal: 3369 harmonic: 3272 Sorted by residual: dihedral pdb=" C4' A B 88 " pdb=" C3' A B 88 " pdb=" C2' A B 88 " pdb=" C1' A B 88 " ideal model delta sinusoidal sigma weight residual 36.34 -36.07 72.42 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' G B 43 " pdb=" C3' G B 43 " pdb=" C2' G B 43 " pdb=" C1' G B 43 " ideal model delta sinusoidal sigma weight residual 36.35 -35.93 72.27 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' U B 63 " pdb=" C3' U B 63 " pdb=" C2' U B 63 " pdb=" C1' U B 63 " ideal model delta sinusoidal sigma weight residual 36.35 -35.76 72.10 1 3.10e+00 1.04e-01 6.92e+02 ... (remaining 6638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1668 0.072 - 0.143: 221 0.143 - 0.214: 61 0.214 - 0.286: 68 0.286 - 0.357: 7 Chirality restraints: 2025 Sorted by residual: chirality pdb=" P G B 43 " pdb=" OP1 G B 43 " pdb=" OP2 G B 43 " pdb=" O5' G B 43 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" P A B 9 " pdb=" OP1 A B 9 " pdb=" OP2 A B 9 " pdb=" O5' A B 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" P G B 39 " pdb=" OP1 G B 39 " pdb=" OP2 G B 39 " pdb=" O5' G B 39 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 2022 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 74 " 0.049 2.00e-02 2.50e+03 2.28e-02 1.42e+01 pdb=" N9 A B 74 " -0.055 2.00e-02 2.50e+03 pdb=" C8 A B 74 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 74 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A B 74 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 74 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A B 74 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A B 74 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A B 74 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 74 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A B 74 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 75 " 0.032 2.00e-02 2.50e+03 1.39e-02 5.35e+00 pdb=" N9 A B 75 " -0.029 2.00e-02 2.50e+03 pdb=" C8 A B 75 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 75 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 75 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A B 75 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 75 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A B 75 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 75 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 75 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 75 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1300 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO A1301 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1301 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1301 " 0.031 5.00e-02 4.00e+02 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3547 2.83 - 3.35: 9228 3.35 - 3.87: 19481 3.87 - 4.38: 20986 4.38 - 4.90: 33652 Nonbonded interactions: 86894 Sorted by model distance: nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.317 3.040 nonbonded pdb=" O ILE A 300 " pdb=" OG SER A 303 " model vdw 2.349 3.040 nonbonded pdb=" O ASP A 483 " pdb=" OG SER A 487 " model vdw 2.356 3.040 nonbonded pdb=" O2' A B 75 " pdb=" O4' A B 76 " model vdw 2.361 3.040 nonbonded pdb=" OG SER A1351 " pdb=" N ILE A1352 " model vdw 2.364 3.120 ... (remaining 86889 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.980 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 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 : 0.006 0.058 11785 Z= 0.372 Angle : 0.862 13.257 16694 Z= 0.507 Chirality : 0.073 0.357 2025 Planarity : 0.005 0.057 1579 Dihedral : 18.689 179.863 4517 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.14 % Allowed : 8.15 % Favored : 91.70 % 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: -4.06 (0.19), residues: 1100 helix: -2.49 (0.16), residues: 526 sheet: -2.08 (0.46), residues: 94 loop : -2.97 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.024 0.002 TYR A 568 PHE 0.017 0.001 PHE A 86 TRP 0.010 0.001 TRP A 476 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.37 (11785) covalent geometry : angle 0.86232 / 0.51 (16694) hydrogen bonds : bond 0.14430 / 9.29 ( 524) hydrogen bonds : angle 5.66219 / 3.84 ( 1405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.371 Fit side-chains REVERT: A 271 TYR cc_start: 0.7215 (t80) cc_final: 0.6945 (t80) REVERT: A 322 ILE cc_start: 0.9262 (pt) cc_final: 0.9003 (mt) REVERT: A 1135 ASP cc_start: 0.8832 (p0) cc_final: 0.8472 (p0) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.0907 time to fit residues: 7.8011 Evaluate side-chains 40 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 37 ASN A 113 HIS A 187 GLN A 295 ASN A 369 GLN A 459 ASN A1262 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.056260 restraints weight = 34598.318| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.73 r_work: 0.2738 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11785 Z= 0.211 Angle : 0.965 19.942 16694 Z= 0.431 Chirality : 0.089 1.122 2025 Planarity : 0.004 0.051 1579 Dihedral : 18.511 177.435 2913 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.72 % Allowed : 10.44 % Favored : 87.84 % 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: -2.17 (0.23), residues: 1100 helix: -0.53 (0.21), residues: 528 sheet: -0.99 (0.58), residues: 70 loop : -2.54 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 494 TYR 0.012 0.001 TYR A 155 PHE 0.028 0.001 PHE A 970 TRP 0.004 0.001 TRP A 659 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (11785) covalent geometry : angle 0.96513 / 0.43 (16694) hydrogen bonds : bond 0.05000 / 3.34 ( 524) hydrogen bonds : angle 4.15870 / 2.81 ( 1405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.393 Fit side-chains REVERT: A 682 PHE cc_start: 0.9051 (m-10) cc_final: 0.8847 (m-80) REVERT: A 733 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 1135 ASP cc_start: 0.9040 (p0) cc_final: 0.8663 (p0) outliers start: 12 outliers final: 6 residues processed: 46 average time/residue: 0.0713 time to fit residues: 5.8514 Evaluate side-chains 42 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.056454 restraints weight = 35117.592| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.69 r_work: 0.2741 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11785 Z= 0.193 Angle : 0.771 11.868 16694 Z= 0.359 Chirality : 0.065 0.774 2025 Planarity : 0.004 0.047 1579 Dihedral : 18.705 177.762 2913 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.29 % Allowed : 12.59 % Favored : 85.12 % 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: -1.51 (0.25), residues: 1100 helix: 0.20 (0.23), residues: 536 sheet: -1.41 (0.54), residues: 87 loop : -2.37 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.009 0.001 TYR A1201 PHE 0.007 0.001 PHE A 478 TRP 0.007 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (11785) covalent geometry : angle 0.77076 / 0.36 (16694) hydrogen bonds : bond 0.04785 / 3.18 ( 524) hydrogen bonds : angle 3.91864 / 2.67 ( 1405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.387 Fit side-chains REVERT: A 733 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 1135 ASP cc_start: 0.9087 (p0) cc_final: 0.8705 (p0) outliers start: 16 outliers final: 10 residues processed: 54 average time/residue: 0.0703 time to fit residues: 6.7879 Evaluate side-chains 48 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 chunk 70 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.079049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.057632 restraints weight = 34839.723| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.74 r_work: 0.2772 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11785 Z= 0.143 Angle : 0.685 9.928 16694 Z= 0.322 Chirality : 0.056 0.576 2025 Planarity : 0.003 0.043 1579 Dihedral : 18.749 174.678 2913 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.15 % Allowed : 13.88 % Favored : 83.98 % 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: -0.97 (0.25), residues: 1100 helix: 0.65 (0.23), residues: 538 sheet: -1.15 (0.55), residues: 87 loop : -2.11 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.016 0.001 TYR A 568 PHE 0.007 0.001 PHE A 478 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (11785) covalent geometry : angle 0.68461 / 0.32 (16694) hydrogen bonds : bond 0.04094 / 2.70 ( 524) hydrogen bonds : angle 3.69404 / 2.53 ( 1405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.438 Fit side-chains REVERT: A 733 ILE cc_start: 0.8452 (tp) cc_final: 0.8066 (tp) REVERT: A 1135 ASP cc_start: 0.9043 (p0) cc_final: 0.8660 (p0) outliers start: 15 outliers final: 8 residues processed: 58 average time/residue: 0.0725 time to fit residues: 7.3698 Evaluate side-chains 54 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1311 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 0.0670 chunk 120 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057120 restraints weight = 34643.588| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.72 r_work: 0.2760 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11785 Z= 0.166 Angle : 0.684 10.230 16694 Z= 0.322 Chirality : 0.054 0.501 2025 Planarity : 0.003 0.043 1579 Dihedral : 18.763 172.130 2913 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.29 % Allowed : 15.02 % Favored : 82.69 % 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: -0.71 (0.26), residues: 1100 helix: 0.90 (0.23), residues: 538 sheet: -0.89 (0.55), residues: 86 loop : -2.05 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.010 0.001 TYR A 568 PHE 0.008 0.001 PHE A 478 TRP 0.007 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (11785) covalent geometry : angle 0.68391 / 0.32 (16694) hydrogen bonds : bond 0.04252 / 2.82 ( 524) hydrogen bonds : angle 3.66677 / 2.51 ( 1405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.364 Fit side-chains REVERT: A 682 PHE cc_start: 0.8886 (m-80) cc_final: 0.8252 (m-80) REVERT: A 733 ILE cc_start: 0.8605 (tp) cc_final: 0.8229 (tp) REVERT: A 1135 ASP cc_start: 0.9051 (p0) cc_final: 0.8669 (p0) outliers start: 16 outliers final: 10 residues processed: 55 average time/residue: 0.0715 time to fit residues: 6.9543 Evaluate side-chains 52 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 75 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.079358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057838 restraints weight = 34725.065| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.74 r_work: 0.2778 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11785 Z= 0.133 Angle : 0.655 10.201 16694 Z= 0.309 Chirality : 0.053 0.476 2025 Planarity : 0.003 0.041 1579 Dihedral : 18.755 170.977 2913 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.29 % Allowed : 15.02 % Favored : 82.69 % 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 (0.26), residues: 1100 helix: 1.07 (0.23), residues: 538 sheet: -0.86 (0.54), residues: 90 loop : -1.99 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 139 TYR 0.010 0.001 TYR A 155 PHE 0.008 0.001 PHE A 478 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (11785) covalent geometry : angle 0.65534 / 0.31 (16694) hydrogen bonds : bond 0.03958 / 2.60 ( 524) hydrogen bonds : angle 3.59443 / 2.46 ( 1405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.363 Fit side-chains REVERT: A 682 PHE cc_start: 0.8898 (m-80) cc_final: 0.8230 (m-80) REVERT: A 733 ILE cc_start: 0.8549 (tp) cc_final: 0.8164 (tp) REVERT: A 1135 ASP cc_start: 0.9041 (p0) cc_final: 0.8660 (p0) outliers start: 16 outliers final: 13 residues processed: 60 average time/residue: 0.0686 time to fit residues: 7.2859 Evaluate side-chains 57 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1311 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057172 restraints weight = 34527.467| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.71 r_work: 0.2762 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 11785 Z= 0.171 Angle : 0.676 9.962 16694 Z= 0.317 Chirality : 0.054 0.471 2025 Planarity : 0.003 0.040 1579 Dihedral : 18.782 169.575 2913 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.58 % Allowed : 15.16 % Favored : 82.26 % 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: -0.46 (0.26), residues: 1100 helix: 1.14 (0.23), residues: 538 sheet: -0.81 (0.54), residues: 90 loop : -1.98 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.011 0.001 TYR A 155 PHE 0.009 0.001 PHE A 478 TRP 0.006 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (11785) covalent geometry : angle 0.67636 / 0.32 (16694) hydrogen bonds : bond 0.04184 / 2.77 ( 524) hydrogen bonds : angle 3.62763 / 2.48 ( 1405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.369 Fit side-chains REVERT: A 682 PHE cc_start: 0.8926 (m-80) cc_final: 0.8239 (m-80) REVERT: A 733 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8204 (tp) REVERT: A 1135 ASP cc_start: 0.9060 (p0) cc_final: 0.8684 (p0) outliers start: 18 outliers final: 16 residues processed: 60 average time/residue: 0.0688 time to fit residues: 7.2187 Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 56 optimal weight: 0.0570 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.078141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.056408 restraints weight = 35008.219| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.75 r_work: 0.2747 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11785 Z= 0.197 Angle : 0.695 9.838 16694 Z= 0.326 Chirality : 0.055 0.476 2025 Planarity : 0.003 0.041 1579 Dihedral : 18.830 167.970 2913 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.86 % Allowed : 15.45 % Favored : 81.69 % 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: -0.40 (0.26), residues: 1100 helix: 1.21 (0.23), residues: 538 sheet: -0.81 (0.54), residues: 90 loop : -1.97 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1333 TYR 0.013 0.001 TYR A 155 PHE 0.009 0.001 PHE A 478 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (11785) covalent geometry : angle 0.69484 / 0.33 (16694) hydrogen bonds : bond 0.04372 / 2.91 ( 524) hydrogen bonds : angle 3.66426 / 2.51 ( 1405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.343 Fit side-chains REVERT: A 733 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8198 (tp) REVERT: A 1135 ASP cc_start: 0.9071 (p0) cc_final: 0.8695 (p0) outliers start: 20 outliers final: 16 residues processed: 59 average time/residue: 0.0696 time to fit residues: 7.0751 Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056065 restraints weight = 34716.686| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.71 r_work: 0.2737 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11785 Z= 0.219 Angle : 0.721 9.736 16694 Z= 0.336 Chirality : 0.056 0.482 2025 Planarity : 0.003 0.041 1579 Dihedral : 18.879 166.969 2913 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.86 % Allowed : 16.02 % Favored : 81.12 % 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: -0.41 (0.26), residues: 1100 helix: 1.22 (0.23), residues: 537 sheet: -0.79 (0.54), residues: 90 loop : -2.00 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1333 TYR 0.014 0.001 TYR A 155 PHE 0.009 0.001 PHE A 478 TRP 0.007 0.001 TRP A 476 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (11785) covalent geometry : angle 0.72095 / 0.34 (16694) hydrogen bonds : bond 0.04583 / 3.05 ( 524) hydrogen bonds : angle 3.73441 / 2.56 ( 1405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.377 Fit side-chains REVERT: A 682 PHE cc_start: 0.8840 (m-80) cc_final: 0.8191 (m-80) REVERT: A 733 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8218 (tp) REVERT: A 1135 ASP cc_start: 0.9080 (p0) cc_final: 0.8705 (p0) outliers start: 20 outliers final: 17 residues processed: 57 average time/residue: 0.0697 time to fit residues: 6.9903 Evaluate side-chains 58 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 86 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.058945 restraints weight = 34583.432| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.74 r_work: 0.2807 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11785 Z= 0.112 Angle : 0.645 9.455 16694 Z= 0.303 Chirality : 0.052 0.467 2025 Planarity : 0.003 0.040 1579 Dihedral : 18.763 167.715 2913 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.29 % Allowed : 17.31 % Favored : 81.40 % 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: -0.11 (0.26), residues: 1100 helix: 1.43 (0.24), residues: 529 sheet: -0.47 (0.55), residues: 90 loop : -1.78 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 664 TYR 0.007 0.001 TYR A 568 PHE 0.010 0.001 PHE A 478 TRP 0.005 0.001 TRP A 659 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (11785) covalent geometry : angle 0.64517 / 0.30 (16694) hydrogen bonds : bond 0.03785 / 2.46 ( 524) hydrogen bonds : angle 3.51076 / 2.41 ( 1405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.370 Fit side-chains REVERT: A 682 PHE cc_start: 0.8846 (m-80) cc_final: 0.8206 (m-80) REVERT: A 733 ILE cc_start: 0.8454 (tp) cc_final: 0.8073 (tp) REVERT: A 1135 ASP cc_start: 0.9029 (p0) cc_final: 0.8647 (p0) outliers start: 9 outliers final: 9 residues processed: 57 average time/residue: 0.0705 time to fit residues: 7.0697 Evaluate side-chains 54 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.079410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.057814 restraints weight = 34652.208| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.73 r_work: 0.2778 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11785 Z= 0.157 Angle : 0.664 9.510 16694 Z= 0.309 Chirality : 0.052 0.442 2025 Planarity : 0.003 0.039 1579 Dihedral : 18.777 166.982 2913 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.57 % Allowed : 17.74 % Favored : 80.69 % 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: -0.12 (0.26), residues: 1100 helix: 1.40 (0.24), residues: 535 sheet: -0.47 (0.56), residues: 90 loop : -1.80 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1333 TYR 0.012 0.001 TYR A 155 PHE 0.009 0.001 PHE A 478 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (11785) covalent geometry : angle 0.66385 / 0.31 (16694) hydrogen bonds : bond 0.04061 / 2.65 ( 524) hydrogen bonds : angle 3.53480 / 2.43 ( 1405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.30 seconds wall clock time: 45 minutes 24.60 seconds (2724.60 seconds total)