Starting phenix.real_space_refine on Wed Mar 4 06:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o0x_0583/03_2026/6o0x_0583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0x_0583/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6o0x_0583/03_2026/6o0x_0583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0x_0583/03_2026/6o0x_0583.map" model { file = "/net/cci-nas-00/data/ceres_data/6o0x_0583/03_2026/6o0x_0583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0x_0583/03_2026/6o0x_0583.cif" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: 2.70, per 1000 atoms: 0.24 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: 0.86 Conformation dependent library (CDL) restraints added in 449.7 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: 1.64 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: 3.43 Time building geometry restraints manager: 1.20 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=" CD LYS A1334 " pdb=" CE LYS A1334 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" C3' A B 8 " pdb=" O3' A B 8 " ideal model delta sigma weight residual 1.417 1.437 -0.020 1.50e-02 4.44e+03 1.69e+00 bond pdb=" C1' DC c 20 " pdb=" N1 DC c 20 " ideal model delta sigma weight residual 1.490 1.526 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CE LYS A1334 " pdb=" NZ LYS A1334 " ideal model delta sigma weight residual 1.489 1.456 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 11780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 16515 2.65 - 5.30: 152 5.30 - 7.95: 23 7.95 - 10.61: 2 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=" 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=" C LYS A1334 " pdb=" CA LYS A1334 " pdb=" CB LYS A1334 " ideal model delta sigma weight residual 109.72 117.55 -7.83 1.73e+00 3.34e-01 2.05e+01 angle pdb=" C3' A B 8 " pdb=" O3' A B 8 " pdb=" P A B 9 " ideal model delta sigma weight residual 120.20 126.08 -5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C GLN A 330 " pdb=" N ASP A 331 " pdb=" CA ASP A 331 " ideal model delta sigma weight residual 121.14 114.28 6.86 1.75e+00 3.27e-01 1.54e+01 ... (remaining 16689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6535 35.97 - 71.95: 395 71.95 - 107.92: 20 107.92 - 143.89: 0 143.89 - 179.86: 3 Dihedral angle restraints: 6953 sinusoidal: 3681 harmonic: 3272 Sorted by residual: dihedral pdb=" CA GLU A 584 " pdb=" C GLU A 584 " pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C4' A B 42 " pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sinusoidal sigma weight residual 220.00 40.14 179.86 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' A B 38 " pdb=" C3' A B 38 " pdb=" O3' A B 38 " pdb=" P G B 39 " ideal model delta sinusoidal sigma weight residual 220.00 43.05 176.95 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 6950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1689 0.057 - 0.114: 288 0.114 - 0.171: 42 0.171 - 0.228: 5 0.228 - 0.285: 1 Chirality restraints: 2025 Sorted by residual: chirality pdb=" C3' A B 8 " pdb=" C4' A B 8 " pdb=" O3' A B 8 " pdb=" C2' A B 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A 48 " pdb=" CA ILE A 48 " pdb=" CG1 ILE A 48 " pdb=" CG2 ILE A 48 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.90e-01 ... (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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.550 Find NCS groups from input model: 0.060 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 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 : 0.005 0.058 11785 Z= 0.259 Angle : 0.737 13.257 16694 Z= 0.402 Chirality : 0.045 0.285 2025 Planarity : 0.005 0.057 1579 Dihedral : 19.360 179.863 4829 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 covalent geometry : bond 0.00547 (11785) covalent geometry : angle 0.73692 (16694) hydrogen bonds : bond 0.14430 ( 524) hydrogen bonds : angle 5.66219 ( 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 : 0.392 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: 0.0932 time to fit residues: 7.7812 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 : 0.313 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 37 ASN A 113 HIS A 187 GLN A 295 ASN A 369 GLN A1262 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055784 restraints weight = 34877.855| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.68 r_work: 0.2723 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11785 Z= 0.186 Angle : 0.533 6.225 16694 Z= 0.293 Chirality : 0.037 0.177 2025 Planarity : 0.004 0.050 1579 Dihedral : 20.530 174.767 3225 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.57 % Allowed : 11.44 % Favored : 86.98 % 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: -2.12 (0.23), residues: 1100 helix: -0.42 (0.21), residues: 533 sheet: -1.67 (0.52), residues: 85 loop : -2.51 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.014 0.001 TYR A 568 PHE 0.011 0.001 PHE A 970 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00395 (11785) covalent geometry : angle 0.53332 (16694) hydrogen bonds : bond 0.04663 ( 524) hydrogen bonds : angle 4.02469 ( 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 53 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.402 Fit side-chains REVERT: A 327 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 1135 ASP cc_start: 0.9068 (p0) cc_final: 0.8698 (p0) outliers start: 11 outliers final: 4 residues processed: 50 average time/residue: 0.0644 time to fit residues: 5.7517 Evaluate side-chains 40 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 LEU 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: 6.9990 chunk 50 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056051 restraints weight = 35051.821| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.69 r_work: 0.2732 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11785 Z= 0.158 Angle : 0.497 6.039 16694 Z= 0.273 Chirality : 0.036 0.183 2025 Planarity : 0.003 0.045 1579 Dihedral : 20.511 174.130 3225 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.15 % Allowed : 13.16 % Favored : 84.69 % 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: -1.30 (0.25), residues: 1100 helix: 0.37 (0.23), residues: 538 sheet: -1.30 (0.55), residues: 85 loop : -2.26 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.014 0.001 TYR A 568 PHE 0.006 0.001 PHE A 970 TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00337 (11785) covalent geometry : angle 0.49663 (16694) hydrogen bonds : bond 0.04223 ( 524) hydrogen bonds : angle 3.77462 ( 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 62 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.352 Fit side-chains REVERT: A 327 GLU cc_start: 0.8230 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 733 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 1135 ASP cc_start: 0.9070 (p0) cc_final: 0.8709 (p0) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.0659 time to fit residues: 6.8262 Evaluate side-chains 49 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ILE 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 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: 1.9990 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.055625 restraints weight = 35143.286| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.69 r_work: 0.2722 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11785 Z= 0.184 Angle : 0.510 6.107 16694 Z= 0.278 Chirality : 0.037 0.179 2025 Planarity : 0.003 0.045 1579 Dihedral : 20.506 172.880 3225 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.15 % Allowed : 13.59 % Favored : 83.26 % 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: -0.97 (0.26), residues: 1100 helix: 0.70 (0.23), residues: 539 sheet: -1.43 (0.53), residues: 89 loop : -2.13 (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 0.007 0.001 PHE A 478 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00395 (11785) covalent geometry : angle 0.51039 (16694) hydrogen bonds : bond 0.04315 ( 524) hydrogen bonds : angle 3.73462 ( 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 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.340 Fit side-chains REVERT: A 327 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8020 (tm-30) REVERT: A 682 PHE cc_start: 0.8945 (m-80) cc_final: 0.8284 (m-80) REVERT: A 733 ILE cc_start: 0.8607 (tp) cc_final: 0.8214 (tp) REVERT: A 1135 ASP cc_start: 0.9073 (p0) cc_final: 0.8713 (p0) outliers start: 22 outliers final: 16 residues processed: 57 average time/residue: 0.0616 time to fit residues: 6.2021 Evaluate side-chains 53 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 472 THR 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 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 962 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1327 PHE Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053128 restraints weight = 35337.849| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.74 r_work: 0.2664 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11785 Z= 0.325 Angle : 0.635 6.728 16694 Z= 0.338 Chirality : 0.042 0.175 2025 Planarity : 0.004 0.044 1579 Dihedral : 20.725 169.920 3225 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.58 % Allowed : 14.31 % Favored : 82.12 % 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: -0.92 (0.26), residues: 1100 helix: 0.78 (0.23), residues: 534 sheet: -1.51 (0.51), residues: 91 loop : -2.10 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1333 TYR 0.019 0.002 TYR A 568 PHE 0.010 0.001 PHE A1204 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00699 (11785) covalent geometry : angle 0.63512 (16694) hydrogen bonds : bond 0.05608 ( 524) hydrogen bonds : angle 4.08663 ( 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 58 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.240 Fit side-chains REVERT: A 327 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 733 ILE cc_start: 0.8748 (tp) cc_final: 0.8539 (tp) REVERT: A 1089 MET cc_start: 0.9331 (mtp) cc_final: 0.9128 (mtp) REVERT: A 1135 ASP cc_start: 0.9093 (p0) cc_final: 0.8728 (p0) outliers start: 25 outliers final: 19 residues processed: 55 average time/residue: 0.0652 time to fit residues: 6.2190 Evaluate side-chains 53 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 472 THR 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 657 THR Chi-restraints excluded: chain A residue 683 LEU 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 962 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1327 PHE 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: 0.9980 chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.055580 restraints weight = 34967.402| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.69 r_work: 0.2721 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1524 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= 0.160 Angle : 0.501 6.203 16694 Z= 0.273 Chirality : 0.037 0.175 2025 Planarity : 0.003 0.043 1579 Dihedral : 20.600 171.620 3225 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.86 % Allowed : 14.59 % Favored : 82.55 % 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: -0.65 (0.26), residues: 1100 helix: 1.01 (0.23), residues: 535 sheet: -1.22 (0.53), residues: 89 loop : -2.00 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1333 TYR 0.012 0.001 TYR A 568 PHE 0.009 0.001 PHE A 478 TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00341 (11785) covalent geometry : angle 0.50124 (16694) hydrogen bonds : bond 0.04254 ( 524) hydrogen bonds : angle 3.70940 ( 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 60 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.387 Fit side-chains REVERT: A 327 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 733 ILE cc_start: 0.8575 (tp) cc_final: 0.8193 (tp) REVERT: A 1135 ASP cc_start: 0.9059 (p0) cc_final: 0.8699 (p0) outliers start: 20 outliers final: 18 residues processed: 58 average time/residue: 0.0776 time to fit residues: 7.4236 Evaluate side-chains 55 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 683 LEU 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 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 1327 PHE Chi-restraints excluded: chain A residue 1342 VAL 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: 0.9990 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 66 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.057347 restraints weight = 34334.143| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.70 r_work: 0.2764 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 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 = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11785 Z= 0.110 Angle : 0.464 5.886 16694 Z= 0.252 Chirality : 0.035 0.178 2025 Planarity : 0.003 0.040 1579 Dihedral : 20.496 173.483 3225 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.58 % Allowed : 15.88 % Favored : 81.55 % 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: -0.31 (0.26), residues: 1100 helix: 1.30 (0.24), residues: 535 sheet: -0.98 (0.53), residues: 91 loop : -1.87 (0.27), residues: 474 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 0.008 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 covalent geometry : bond 0.00230 (11785) covalent geometry : angle 0.46353 (16694) hydrogen bonds : bond 0.03658 ( 524) hydrogen bonds : angle 3.51718 ( 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 64 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.378 Fit side-chains REVERT: A 327 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 682 PHE cc_start: 0.8892 (m-80) cc_final: 0.8253 (m-80) REVERT: A 733 ILE cc_start: 0.8534 (tp) cc_final: 0.8163 (tp) REVERT: A 1135 ASP cc_start: 0.9033 (p0) cc_final: 0.8666 (p0) outliers start: 18 outliers final: 16 residues processed: 59 average time/residue: 0.0677 time to fit residues: 7.1146 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 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 616 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 1108 GLU Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.079146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057582 restraints weight = 34362.556| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.70 r_work: 0.2770 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 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 = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11785 Z= 0.109 Angle : 0.464 7.502 16694 Z= 0.250 Chirality : 0.035 0.178 2025 Planarity : 0.003 0.038 1579 Dihedral : 20.474 173.367 3225 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.43 % Allowed : 16.02 % Favored : 81.55 % 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: -0.14 (0.26), residues: 1100 helix: 1.41 (0.23), residues: 537 sheet: -0.71 (0.55), residues: 90 loop : -1.81 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 664 TYR 0.010 0.001 TYR A 155 PHE 0.009 0.001 PHE A 478 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00228 (11785) covalent geometry : angle 0.46400 (16694) hydrogen bonds : bond 0.03578 ( 524) hydrogen bonds : angle 3.45334 ( 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 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.385 Fit side-chains REVERT: A 327 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8064 (tm-30) REVERT: A 682 PHE cc_start: 0.8903 (m-80) cc_final: 0.8240 (m-80) REVERT: A 733 ILE cc_start: 0.8525 (tp) cc_final: 0.8151 (tp) REVERT: A 1135 ASP cc_start: 0.9030 (p0) cc_final: 0.8661 (p0) outliers start: 17 outliers final: 15 residues processed: 61 average time/residue: 0.0676 time to fit residues: 7.2365 Evaluate side-chains 61 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 58 THR 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 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 Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.055684 restraints weight = 34487.705| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.70 r_work: 0.2722 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11785 Z= 0.179 Angle : 0.515 8.415 16694 Z= 0.275 Chirality : 0.037 0.173 2025 Planarity : 0.003 0.039 1579 Dihedral : 20.530 170.503 3225 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.72 % Allowed : 16.17 % 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: -0.12 (0.26), residues: 1100 helix: 1.43 (0.23), residues: 537 sheet: -0.84 (0.54), residues: 92 loop : -1.77 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.014 0.001 TYR A 155 PHE 0.009 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 covalent geometry : bond 0.00385 (11785) covalent geometry : angle 0.51498 (16694) hydrogen bonds : bond 0.04255 ( 524) hydrogen bonds : angle 3.59224 ( 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 60 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.231 Fit side-chains REVERT: A 327 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 682 PHE cc_start: 0.8903 (m-80) cc_final: 0.8214 (m-80) REVERT: A 733 ILE cc_start: 0.8574 (tp) cc_final: 0.8197 (tp) REVERT: A 1135 ASP cc_start: 0.9054 (p0) cc_final: 0.8687 (p0) outliers start: 19 outliers final: 18 residues processed: 58 average time/residue: 0.0657 time to fit residues: 6.7197 Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 595 HIS 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 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 1327 PHE 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: 0.1980 chunk 28 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059479 restraints weight = 34438.138| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.73 r_work: 0.2816 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 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 = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11785 Z= 0.092 Angle : 0.455 10.253 16694 Z= 0.243 Chirality : 0.034 0.176 2025 Planarity : 0.003 0.036 1579 Dihedral : 20.399 174.155 3225 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.00 % Allowed : 16.88 % 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: 0.17 (0.26), residues: 1100 helix: 1.63 (0.24), residues: 541 sheet: -0.52 (0.55), residues: 90 loop : -1.63 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 78 TYR 0.008 0.001 TYR A 155 PHE 0.008 0.001 PHE A 478 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.000 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00189 (11785) covalent geometry : angle 0.45502 (16694) hydrogen bonds : bond 0.03228 ( 524) hydrogen bonds : angle 3.35420 ( 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 64 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.312 Fit side-chains REVERT: A 327 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 733 ILE cc_start: 0.8461 (tp) cc_final: 0.8100 (tp) REVERT: A 962 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8956 (tt) REVERT: A 1135 ASP cc_start: 0.9023 (p0) cc_final: 0.8640 (p0) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.0725 time to fit residues: 7.5121 Evaluate side-chains 60 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 472 THR 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 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 1311 HIS Chi-restraints excluded: chain A residue 1327 PHE 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: 0.6980 chunk 35 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.078564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.056695 restraints weight = 34805.755| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.73 r_work: 0.2749 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11785 Z= 0.150 Angle : 0.486 6.507 16694 Z= 0.262 Chirality : 0.036 0.169 2025 Planarity : 0.003 0.037 1579 Dihedral : 20.433 170.518 3225 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.72 % Allowed : 17.60 % 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: 0.18 (0.26), residues: 1100 helix: 1.65 (0.24), residues: 540 sheet: -0.49 (0.55), residues: 90 loop : -1.66 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1333 TYR 0.013 0.001 TYR A 155 PHE 0.009 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 covalent geometry : bond 0.00320 (11785) covalent geometry : angle 0.48577 (16694) hydrogen bonds : bond 0.03932 ( 524) hydrogen bonds : angle 3.44623 ( 1405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2501.81 seconds wall clock time: 43 minutes 26.34 seconds (2606.34 seconds total)