Starting phenix.real_space_refine on Thu Feb 15 02:51:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4u_16429/02_2024/8c4u_16429.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4u_16429/02_2024/8c4u_16429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4u_16429/02_2024/8c4u_16429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4u_16429/02_2024/8c4u_16429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4u_16429/02_2024/8c4u_16429.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4u_16429/02_2024/8c4u_16429.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 6895 2.51 5 N 1843 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A PHE 1132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10952 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1260, 10142 Classifications: {'peptide': 1260} Link IDs: {'PTRANS': 39, 'TRANS': 1220} Chain breaks: 8 Chain: "H" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 429 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "T" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 380 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.31, per 1000 atoms: 0.58 Number of scatterers: 10952 At special positions: 0 Unit cell: (97.9, 101.2, 119.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 38 15.00 Mg 1 11.99 O 2120 8.00 N 1843 7.00 C 6895 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 - 3.50 Amino acid : False - 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: 4.95 Conformation dependent library (CDL) restraints added in 2.0 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 58.0% alpha, 12.1% beta 9 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.818A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 279 removed outlier: 4.260A pdb=" N CYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 324 removed outlier: 3.595A pdb=" N ILE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.809A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.426A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.716A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 removed outlier: 3.523A pdb=" N PHE A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 635 removed outlier: 3.732A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.560A pdb=" N LEU A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 674 removed outlier: 3.927A pdb=" N VAL A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 3.814A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 735 through 760 removed outlier: 3.726A pdb=" N ALA A 739 " --> pdb=" O MET A 735 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.847A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 Processing helix chain 'A' and resid 848 through 858 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 removed outlier: 3.718A pdb=" N ILE A 915 " --> pdb=" O TYR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 947 removed outlier: 4.358A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 3.984A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1012 Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1061 through 1084 removed outlier: 3.802A pdb=" N SER A1066 " --> pdb=" O ASN A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1127 Processing helix chain 'A' and resid 1128 through 1134 removed outlier: 3.895A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.806A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1190 Processing helix chain 'A' and resid 1191 through 1193 No H-bonds generated for 'chain 'A' and resid 1191 through 1193' Processing helix chain 'A' and resid 1200 through 1219 removed outlier: 3.780A pdb=" N CYS A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1255 removed outlier: 4.255A pdb=" N TYR A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.522A pdb=" N LEU A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1365 removed outlier: 3.552A pdb=" N SER A1363 " --> pdb=" O GLU A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1370 removed outlier: 3.521A pdb=" N ASP A1369 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1389 Processing helix chain 'A' and resid 1389 through 1398 removed outlier: 3.603A pdb=" N ALA A1395 " --> pdb=" O SER A1391 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A1398 " --> pdb=" O THR A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1411 Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.798A pdb=" N VAL A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1457 removed outlier: 3.628A pdb=" N THR A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1470 Processing helix chain 'A' and resid 1506 through 1511 removed outlier: 3.513A pdb=" N PHE A1511 " --> pdb=" O ILE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1583 through 1592 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.927A pdb=" N THR A 529 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.421A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.141A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1168 through 1171 removed outlier: 3.805A pdb=" N PHE A1175 " --> pdb=" O SER A1182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 4.268A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1485 through 1489 562 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1668 1.30 - 1.43: 3239 1.43 - 1.56: 6198 1.56 - 1.68: 73 1.68 - 1.81: 91 Bond restraints: 11269 Sorted by residual: bond pdb=" C ARG A 904 " pdb=" O ARG A 904 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.15e-02 7.56e+03 3.11e+01 bond pdb=" C TRP A 498 " pdb=" O TRP A 498 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.28e-02 6.10e+03 2.50e+01 bond pdb=" CA SER A1133 " pdb=" CB SER A1133 " ideal model delta sigma weight residual 1.528 1.467 0.060 1.35e-02 5.49e+03 2.00e+01 bond pdb=" C ASP A 348 " pdb=" O ASP A 348 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.15e-02 7.56e+03 1.83e+01 bond pdb=" CA SER A1192 " pdb=" CB SER A1192 " ideal model delta sigma weight residual 1.532 1.462 0.070 1.78e-02 3.16e+03 1.53e+01 ... (remaining 11264 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.07: 393 106.07 - 113.17: 6140 113.17 - 120.27: 4200 120.27 - 127.37: 4492 127.37 - 134.48: 178 Bond angle restraints: 15403 Sorted by residual: angle pdb=" N GLU A 719 " pdb=" CA GLU A 719 " pdb=" C GLU A 719 " ideal model delta sigma weight residual 113.41 104.49 8.92 1.22e+00 6.72e-01 5.34e+01 angle pdb=" O TYR A 701 " pdb=" C TYR A 701 " pdb=" N PRO A 702 " ideal model delta sigma weight residual 121.27 117.25 4.02 6.00e-01 2.78e+00 4.50e+01 angle pdb=" N TRP A1338 " pdb=" CA TRP A1338 " pdb=" C TRP A1338 " ideal model delta sigma weight residual 114.56 106.44 8.12 1.27e+00 6.20e-01 4.09e+01 angle pdb=" N ILE A 717 " pdb=" CA ILE A 717 " pdb=" C ILE A 717 " ideal model delta sigma weight residual 113.00 105.34 7.66 1.30e+00 5.92e-01 3.47e+01 angle pdb=" N TRP A 584 " pdb=" CA TRP A 584 " pdb=" C TRP A 584 " ideal model delta sigma weight residual 111.07 105.19 5.88 1.07e+00 8.73e-01 3.02e+01 ... (remaining 15398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 6419 31.66 - 63.32: 331 63.32 - 94.98: 27 94.98 - 126.65: 1 126.65 - 158.31: 2 Dihedral angle restraints: 6780 sinusoidal: 3075 harmonic: 3705 Sorted by residual: dihedral pdb=" O4' U H 7 " pdb=" C1' U H 7 " pdb=" N1 U H 7 " pdb=" C2 U H 7 " ideal model delta sinusoidal sigma weight residual 200.00 41.69 158.31 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" C TYR A1368 " pdb=" N TYR A1368 " pdb=" CA TYR A1368 " pdb=" CB TYR A1368 " ideal model delta harmonic sigma weight residual -122.60 -132.89 10.29 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" O4' U T 24 " pdb=" C1' U T 24 " pdb=" N1 U T 24 " pdb=" C2 U T 24 " ideal model delta sinusoidal sigma weight residual -160.00 -107.45 -52.55 1 1.50e+01 4.44e-03 1.67e+01 ... (remaining 6777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1675 0.106 - 0.213: 62 0.213 - 0.319: 8 0.319 - 0.426: 2 0.426 - 0.532: 1 Chirality restraints: 1748 Sorted by residual: chirality pdb=" P A H 2 " pdb=" OP1 A H 2 " pdb=" OP2 A H 2 " pdb=" O5' A H 2 " both_signs ideal model delta sigma weight residual True 2.41 -1.88 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA LYS A1415 " pdb=" N LYS A1415 " pdb=" C LYS A1415 " pdb=" CB LYS A1415 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA TRP A 817 " pdb=" N TRP A 817 " pdb=" C TRP A 817 " pdb=" CB TRP A 817 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 1745 not shown) Planarity restraints: 1799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A1413 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C HIS A1413 " 0.071 2.00e-02 2.50e+03 pdb=" O HIS A1413 " -0.026 2.00e-02 2.50e+03 pdb=" N MET A1414 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1191 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C GLY A1191 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY A1191 " 0.024 2.00e-02 2.50e+03 pdb=" N SER A1192 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1196 " -0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A1197 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A1197 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1197 " -0.050 5.00e-02 4.00e+02 ... (remaining 1796 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 111 2.63 - 3.19: 9674 3.19 - 3.76: 17343 3.76 - 4.33: 24026 4.33 - 4.90: 39995 Nonbonded interactions: 91149 Sorted by model distance: nonbonded pdb=" OD1 ASP A1099 " pdb="MG MG A2201 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR A 328 " pdb=" OG1 THR A 545 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR A1306 " pdb=" OD1 ASN A1434 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR A 341 " pdb=" OH TYR A 353 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR A 912 " pdb=" OG1 THR A 989 " model vdw 2.252 2.440 ... (remaining 91144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.270 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: 0.020 Extract box with map and model: 3.990 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 36.360 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 0.070 11269 Z= 0.303 Angle : 0.744 8.917 15403 Z= 0.473 Chirality : 0.049 0.532 1748 Planarity : 0.004 0.091 1799 Dihedral : 17.893 158.308 4380 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.81 % Allowed : 20.14 % Favored : 79.05 % Cbeta Deviations : 0.08 % 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: 0.43 (0.24), residues: 1242 helix: 1.30 (0.20), residues: 667 sheet: -0.25 (0.49), residues: 103 loop : -1.03 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 584 HIS 0.006 0.001 HIS A1413 PHE 0.015 0.001 PHE A 585 TYR 0.020 0.001 TYR A1104 ARG 0.004 0.000 ARG A 904 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.216 Fit side-chains REVERT: A 1429 VAL cc_start: 0.7153 (t) cc_final: 0.6934 (t) outliers start: 9 outliers final: 2 residues processed: 124 average time/residue: 0.2142 time to fit residues: 39.7057 Evaluate side-chains 117 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 1112 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11269 Z= 0.170 Angle : 0.498 7.064 15403 Z= 0.256 Chirality : 0.036 0.166 1748 Planarity : 0.004 0.068 1799 Dihedral : 15.343 158.213 1938 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.25 % Allowed : 19.69 % Favored : 78.06 % 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: 0.97 (0.24), residues: 1242 helix: 1.84 (0.20), residues: 676 sheet: -0.01 (0.50), residues: 103 loop : -1.02 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.004 0.001 HIS A1413 PHE 0.015 0.001 PHE A 585 TYR 0.010 0.001 TYR A1509 ARG 0.003 0.000 ARG A1407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 349 MET cc_start: 0.8174 (mmm) cc_final: 0.7897 (tpp) REVERT: A 617 MET cc_start: 0.8678 (tpt) cc_final: 0.8428 (tpt) REVERT: A 1361 TRP cc_start: 0.7489 (t60) cc_final: 0.7093 (t60) outliers start: 25 outliers final: 14 residues processed: 139 average time/residue: 0.2239 time to fit residues: 46.3380 Evaluate side-chains 127 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1424 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1409 GLN A1413 HIS A1480 GLN A1575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11269 Z= 0.224 Angle : 0.498 7.210 15403 Z= 0.255 Chirality : 0.036 0.148 1748 Planarity : 0.003 0.062 1799 Dihedral : 15.329 158.217 1936 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.88 % Allowed : 19.42 % Favored : 77.70 % 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: 1.03 (0.24), residues: 1242 helix: 1.87 (0.20), residues: 678 sheet: -0.04 (0.50), residues: 103 loop : -0.96 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.004 0.001 HIS A1148 PHE 0.015 0.001 PHE A 585 TYR 0.013 0.001 TYR A 352 ARG 0.005 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 349 MET cc_start: 0.8077 (mmm) cc_final: 0.7869 (tpp) REVERT: A 617 MET cc_start: 0.8805 (tpt) cc_final: 0.8577 (tpt) REVERT: A 1341 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7420 (m-10) REVERT: A 1361 TRP cc_start: 0.7498 (t60) cc_final: 0.7077 (t60) REVERT: A 1412 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7004 (pt0) outliers start: 32 outliers final: 22 residues processed: 141 average time/residue: 0.1936 time to fit residues: 41.1923 Evaluate side-chains 134 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1341 PHE Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1412 GLN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1475 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 78 optimal weight: 0.0070 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11269 Z= 0.187 Angle : 0.477 7.214 15403 Z= 0.243 Chirality : 0.036 0.142 1748 Planarity : 0.003 0.056 1799 Dihedral : 15.274 158.436 1936 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.97 % Allowed : 20.14 % Favored : 76.89 % 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: 1.15 (0.24), residues: 1242 helix: 1.97 (0.20), residues: 678 sheet: 0.07 (0.50), residues: 103 loop : -0.91 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.002 0.001 HIS A1148 PHE 0.014 0.001 PHE A 894 TYR 0.011 0.001 TYR A1509 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 617 MET cc_start: 0.8834 (tpt) cc_final: 0.8622 (tpt) REVERT: A 1341 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7477 (m-10) REVERT: A 1361 TRP cc_start: 0.7499 (t60) cc_final: 0.7134 (t60) REVERT: A 1412 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6883 (pt0) outliers start: 33 outliers final: 22 residues processed: 144 average time/residue: 0.2049 time to fit residues: 44.7850 Evaluate side-chains 135 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1132 PHE Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1341 PHE Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1412 GLN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11269 Z= 0.392 Angle : 0.585 9.213 15403 Z= 0.297 Chirality : 0.039 0.160 1748 Planarity : 0.004 0.059 1799 Dihedral : 15.391 158.038 1936 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.96 % Allowed : 19.06 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.24), residues: 1242 helix: 1.59 (0.20), residues: 685 sheet: 0.02 (0.49), residues: 104 loop : -1.06 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 473 HIS 0.006 0.001 HIS A1148 PHE 0.017 0.002 PHE A 585 TYR 0.022 0.002 TYR A 352 ARG 0.004 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 102 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 363 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: A 617 MET cc_start: 0.8992 (tpt) cc_final: 0.8754 (tpt) REVERT: A 1072 MET cc_start: 0.9281 (mmm) cc_final: 0.8613 (mmm) REVERT: A 1341 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7699 (m-10) REVERT: A 1412 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6842 (pt0) outliers start: 44 outliers final: 31 residues processed: 143 average time/residue: 0.1938 time to fit residues: 41.4220 Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1341 PHE Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1412 GLN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1514 THR Chi-restraints excluded: chain A residue 1581 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11269 Z= 0.216 Angle : 0.500 7.595 15403 Z= 0.254 Chirality : 0.036 0.144 1748 Planarity : 0.003 0.055 1799 Dihedral : 15.311 158.894 1936 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.79 % Allowed : 21.04 % Favored : 76.17 % 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 (0.24), residues: 1242 helix: 1.76 (0.20), residues: 685 sheet: -0.08 (0.49), residues: 103 loop : -1.03 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.002 0.001 HIS A1049 PHE 0.016 0.001 PHE A 894 TYR 0.016 0.001 TYR A1253 ARG 0.007 0.000 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 1341 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: A 1412 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6856 (pt0) outliers start: 31 outliers final: 24 residues processed: 136 average time/residue: 0.1743 time to fit residues: 35.1544 Evaluate side-chains 130 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1332 PHE Chi-restraints excluded: chain A residue 1341 PHE Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1412 GLN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1581 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: