Starting phenix.real_space_refine on Tue Jul 29 14:59:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o0x_0583/07_2025/6o0x_0583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0x_0583/07_2025/6o0x_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_0583/07_2025/6o0x_0583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0x_0583/07_2025/6o0x_0583.map" model { file = "/net/cci-nas-00/data/ceres_data/6o0x_0583/07_2025/6o0x_0583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0x_0583/07_2025/6o0x_0583.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 15, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 19, 'ASP:plan': 40, 'PHE:plan': 5, 'GLU:plan': 62, 'ARG:plan': 12} 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: 7.81, per 1000 atoms: 0.69 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 6.01 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: 10.03 Time building geometry restraints manager: 3.68 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: 84.890 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 38.030 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP A 476 HIS 0.009 0.001 HIS A 328 PHE 0.017 0.001 PHE A 86 TYR 0.024 0.002 TYR A 568 ARG 0.004 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.14430 ( 524) hydrogen bonds : angle 5.66219 ( 1405) covalent geometry : bond 0.00547 (11785) covalent geometry : angle 0.73692 (16694) *********************** 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 : 1.103 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: 0.2294 time to fit residues: 19.4857 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 : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 0.0570 chunk 52 optimal weight: 0.0270 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 0.0020 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.5766 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.079850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058563 restraints weight = 34003.137| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.71 r_work: 0.2791 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11785 Z= 0.101 Angle : 0.475 6.442 16694 Z= 0.262 Chirality : 0.034 0.187 2025 Planarity : 0.004 0.047 1579 Dihedral : 20.415 177.662 3225 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.00 % Allowed : 10.44 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.23), residues: 1100 helix: -0.57 (0.21), residues: 539 sheet: -1.49 (0.53), residues: 85 loop : -2.48 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.013 0.001 PHE A 970 TYR 0.008 0.001 TYR A 568 ARG 0.002 0.000 ARG A 664 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 524) hydrogen bonds : angle 3.92165 ( 1405) covalent geometry : bond 0.00202 (11785) covalent geometry : angle 0.47485 (16694) *********************** 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 68 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.015 Fit side-chains REVERT: A 109 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8902 (mp0) REVERT: A 322 ILE cc_start: 0.9192 (pt) cc_final: 0.8972 (mt) REVERT: A 327 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 962 LEU cc_start: 0.9314 (mt) cc_final: 0.8860 (tt) REVERT: A 1135 ASP cc_start: 0.8994 (p0) cc_final: 0.8606 (p0) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.1872 time to fit residues: 19.6363 Evaluate side-chains 52 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 750 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.075030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.053355 restraints weight = 35462.881| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.75 r_work: 0.2665 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- 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 = 0.91 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 = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 11785 Z= 0.341 Angle : 0.652 6.690 16694 Z= 0.348 Chirality : 0.042 0.177 2025 Planarity : 0.004 0.046 1579 Dihedral : 20.713 170.777 3225 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.86 % Allowed : 13.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.25), residues: 1100 helix: 0.23 (0.23), residues: 533 sheet: -1.59 (0.52), residues: 89 loop : -2.27 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.011 0.002 PHE A 491 TYR 0.020 0.002 TYR A 568 ARG 0.005 0.001 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.05741 ( 524) hydrogen bonds : angle 4.15067 ( 1405) covalent geometry : bond 0.00736 (11785) covalent geometry : angle 0.65171 (16694) *********************** 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 56 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 1.271 Fit side-chains REVERT: A 327 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 682 PHE cc_start: 0.9069 (m-80) cc_final: 0.8810 (m-80) REVERT: A 733 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 1135 ASP cc_start: 0.9104 (p0) cc_final: 0.8746 (p0) outliers start: 20 outliers final: 13 residues processed: 52 average time/residue: 0.3048 time to fit residues: 26.9428 Evaluate side-chains 45 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 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 1310 ILE Chi-restraints excluded: chain A residue 1327 PHE 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 119 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.078136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.056666 restraints weight = 34309.243| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.67 r_work: 0.2748 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- 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 = 0.99 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: 0.8723 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11785 Z= 0.127 Angle : 0.475 5.843 16694 Z= 0.260 Chirality : 0.035 0.177 2025 Planarity : 0.003 0.044 1579 Dihedral : 20.507 173.571 3225 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.29 % Allowed : 14.31 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1100 helix: 0.75 (0.23), residues: 533 sheet: -1.46 (0.53), residues: 91 loop : -2.07 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.008 0.001 PHE A 478 TYR 0.010 0.001 TYR A 568 ARG 0.003 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 524) hydrogen bonds : angle 3.62663 ( 1405) covalent geometry : bond 0.00266 (11785) covalent geometry : angle 0.47533 (16694) *********************** 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: 16 poor density : 43 time to evaluate : 1.174 Fit side-chains REVERT: A 327 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 733 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8145 (tp) REVERT: A 1135 ASP cc_start: 0.9041 (p0) cc_final: 0.8670 (p0) outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 0.2062 time to fit residues: 20.1038 Evaluate side-chains 50 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 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 1311 HIS Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.075302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.053491 restraints weight = 34993.983| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.73 r_work: 0.2675 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 11785 Z= 0.304 Angle : 0.607 6.620 16694 Z= 0.324 Chirality : 0.041 0.173 2025 Planarity : 0.004 0.044 1579 Dihedral : 20.687 168.661 3225 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.29 % Allowed : 14.74 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.26), residues: 1100 helix: 0.86 (0.23), residues: 534 sheet: -1.39 (0.52), residues: 88 loop : -2.04 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A1134 TYR 0.019 0.002 TYR A 568 ARG 0.003 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 524) hydrogen bonds : angle 3.96628 ( 1405) covalent geometry : bond 0.00652 (11785) covalent geometry : angle 0.60660 (16694) *********************** 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 56 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 1.558 Fit side-chains REVERT: A 327 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 733 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 1089 MET cc_start: 0.9290 (mtp) cc_final: 0.9059 (mtp) REVERT: A 1135 ASP cc_start: 0.9096 (p0) cc_final: 0.8737 (p0) outliers start: 23 outliers final: 19 residues processed: 52 average time/residue: 0.2609 time to fit residues: 23.6631 Evaluate side-chains 53 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 ILE 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 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 962 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1310 ILE 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 53 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.076249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.054443 restraints weight = 35512.392| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.72 r_work: 0.2694 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 11785 Z= 0.216 Angle : 0.538 6.442 16694 Z= 0.291 Chirality : 0.038 0.174 2025 Planarity : 0.003 0.044 1579 Dihedral : 20.657 169.791 3225 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.15 % Allowed : 14.88 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1100 helix: 1.02 (0.23), residues: 535 sheet: -1.16 (0.53), residues: 88 loop : -1.97 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.010 0.001 PHE A1134 TYR 0.015 0.001 TYR A 568 ARG 0.002 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 524) hydrogen bonds : angle 3.81547 ( 1405) covalent geometry : bond 0.00463 (11785) covalent geometry : angle 0.53787 (16694) *********************** 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 56 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 1.095 Fit side-chains REVERT: A 327 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 733 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8226 (tp) REVERT: A 1089 MET cc_start: 0.9269 (mtp) cc_final: 0.9049 (mtp) REVERT: A 1135 ASP cc_start: 0.9078 (p0) cc_final: 0.8716 (p0) outliers start: 22 outliers final: 17 residues processed: 54 average time/residue: 0.1826 time to fit residues: 16.5564 Evaluate side-chains 53 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 ILE 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 595 HIS 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 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 1098 THR Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9990 chunk 25 optimal weight: 50.0000 chunk 30 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.077530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.055952 restraints weight = 35178.126| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.71 r_work: 0.2727 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 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 = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11785 Z= 0.150 Angle : 0.490 6.019 16694 Z= 0.266 Chirality : 0.036 0.174 2025 Planarity : 0.003 0.041 1579 Dihedral : 20.582 171.311 3225 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.15 % Allowed : 15.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1100 helix: 1.21 (0.24), residues: 535 sheet: -0.98 (0.54), residues: 88 loop : -1.87 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.010 0.001 PHE A 478 TYR 0.012 0.001 TYR A 568 ARG 0.002 0.000 ARG A1333 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 524) hydrogen bonds : angle 3.64771 ( 1405) covalent geometry : bond 0.00320 (11785) covalent geometry : angle 0.49047 (16694) *********************** 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 66 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 733 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8164 (tp) REVERT: A 1135 ASP cc_start: 0.9060 (p0) cc_final: 0.8699 (p0) outliers start: 22 outliers final: 17 residues processed: 62 average time/residue: 0.1662 time to fit residues: 17.9057 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 : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU 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 472 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 597 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 1098 THR Chi-restraints excluded: chain A residue 1327 PHE 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 93 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.053366 restraints weight = 35566.727| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.80 r_work: 0.2663 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 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 = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 11785 Z= 0.328 Angle : 0.630 6.815 16694 Z= 0.334 Chirality : 0.042 0.170 2025 Planarity : 0.004 0.043 1579 Dihedral : 20.766 167.550 3225 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.01 % Allowed : 15.16 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1100 helix: 1.05 (0.24), residues: 532 sheet: -1.17 (0.52), residues: 93 loop : -1.94 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 412 PHE 0.011 0.001 PHE A1134 TYR 0.020 0.002 TYR A 568 ARG 0.004 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.05478 ( 524) hydrogen bonds : angle 4.05121 ( 1405) covalent geometry : bond 0.00708 (11785) covalent geometry : angle 0.63036 (16694) *********************** 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 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 35 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 733 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8229 (tp) REVERT: A 1135 ASP cc_start: 0.9087 (p0) cc_final: 0.8742 (p0) outliers start: 28 outliers final: 26 residues processed: 60 average time/residue: 0.1538 time to fit residues: 16.1233 Evaluate side-chains 62 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 35 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 58 THR 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 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 548 ILE Chi-restraints excluded: chain A residue 568 TYR 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 657 THR 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 1310 ILE Chi-restraints excluded: chain A residue 1327 PHE 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 3 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.0570 chunk 92 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.078011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056251 restraints weight = 35033.117| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.75 r_work: 0.2741 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 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 = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11785 Z= 0.134 Angle : 0.482 5.836 16694 Z= 0.262 Chirality : 0.036 0.172 2025 Planarity : 0.003 0.044 1579 Dihedral : 20.596 171.730 3225 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.00 % Allowed : 15.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1100 helix: 1.33 (0.24), residues: 532 sheet: -0.88 (0.53), residues: 93 loop : -1.77 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.009 0.001 PHE A1134 TYR 0.013 0.001 TYR A 568 ARG 0.001 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 524) hydrogen bonds : angle 3.58175 ( 1405) covalent geometry : bond 0.00283 (11785) covalent geometry : angle 0.48194 (16694) *********************** 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 68 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 682 PHE cc_start: 0.8879 (m-80) cc_final: 0.8268 (m-80) REVERT: A 733 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8109 (tp) REVERT: A 1135 ASP cc_start: 0.9052 (p0) cc_final: 0.8692 (p0) outliers start: 21 outliers final: 19 residues processed: 63 average time/residue: 0.1634 time to fit residues: 17.8214 Evaluate side-chains 64 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU 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 472 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 568 TYR 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 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 1098 THR 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 14 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 87 optimal weight: 0.0370 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 1.9462 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.077857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056278 restraints weight = 34361.593| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.66 r_work: 0.2739 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 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 = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1835 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= 0.147 Angle : 0.492 7.303 16694 Z= 0.266 Chirality : 0.036 0.173 2025 Planarity : 0.003 0.039 1579 Dihedral : 20.588 171.171 3225 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.00 % Allowed : 16.02 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1100 helix: 1.40 (0.24), residues: 533 sheet: -0.72 (0.51), residues: 101 loop : -1.73 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.004 0.001 HIS A 328 PHE 0.009 0.001 PHE A 478 TYR 0.013 0.001 TYR A 568 ARG 0.002 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 524) hydrogen bonds : angle 3.57263 ( 1405) covalent geometry : bond 0.00314 (11785) covalent geometry : angle 0.49203 (16694) ********************** 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 66 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 682 PHE cc_start: 0.8864 (m-80) cc_final: 0.8236 (m-80) REVERT: A 733 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8229 (tp) REVERT: A 1135 ASP cc_start: 0.9063 (p0) cc_final: 0.8685 (p0) outliers start: 21 outliers final: 19 residues processed: 62 average time/residue: 0.1578 time to fit residues: 17.0230 Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 472 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 568 TYR 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 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 1098 THR 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 50 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.076177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.054313 restraints weight = 34779.199| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.75 r_work: 0.2686 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11785 Z= 0.262 Angle : 0.577 6.731 16694 Z= 0.308 Chirality : 0.040 0.168 2025 Planarity : 0.003 0.041 1579 Dihedral : 20.680 167.617 3225 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.86 % Allowed : 16.31 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1100 helix: 1.25 (0.24), residues: 533 sheet: -0.76 (0.53), residues: 93 loop : -1.79 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 478 TYR 0.018 0.001 TYR A 568 ARG 0.003 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 524) hydrogen bonds : angle 3.85178 ( 1405) covalent geometry : bond 0.00562 (11785) covalent geometry : angle 0.57704 (16694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6365.59 seconds wall clock time: 116 minutes 48.52 seconds (7008.52 seconds total)