Starting phenix.real_space_refine on Fri Sep 11 22:32:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.map" model { file = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oeb_12863/09_2026/7oeb_12863.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 7425 2.51 5 N 1967 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11682 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 11549 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1434, 11539 Classifications: {'peptide': 1434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1387} Chain breaks: 11 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1434, 11539 Classifications: {'peptide': 1434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1387} Chain breaks: 11 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 11745 Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNAv2': 6} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2483 SG CYS L 321 38.338 100.395 64.570 1.00 54.49 S ATOM 2860 SG CYS L 366 38.027 99.920 68.094 1.00 69.97 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS L1435 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS L1435 " occ=0.50 Time building chain proxies: 3.97, per 1000 atoms: 0.34 Number of scatterers: 11682 At special positions: 0 Unit cell: (118.261, 131.493, 101.721, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 6 15.00 Mg 2 11.99 O 2208 8.00 N 1967 7.00 C 7425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 840.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 59.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 19 through 32 removed outlier: 4.550A pdb=" N ARG L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 58 Processing helix chain 'L' and resid 68 through 76 Processing helix chain 'L' and resid 108 through 131 Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 153 through 175 Processing helix chain 'L' and resid 179 through 191 Processing helix chain 'L' and resid 199 through 204 Processing helix chain 'L' and resid 211 through 223 removed outlier: 3.731A pdb=" N GLU L 215 " --> pdb=" O SER L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 251 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 273 through 275 No H-bonds generated for 'chain 'L' and resid 273 through 275' Processing helix chain 'L' and resid 284 through 293 Processing helix chain 'L' and resid 296 through 303 Processing helix chain 'L' and resid 321 through 336 removed outlier: 3.533A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 365 Processing helix chain 'L' and resid 385 through 404 Processing helix chain 'L' and resid 412 through 435 removed outlier: 3.527A pdb=" N ASP L 434 " --> pdb=" O ALA L 430 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL L 435 " --> pdb=" O ALA L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 442 Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.614A pdb=" N VAL L 448 " --> pdb=" O ASN L 445 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 459 Processing helix chain 'L' and resid 491 through 507 Processing helix chain 'L' and resid 508 through 510 No H-bonds generated for 'chain 'L' and resid 508 through 510' Processing helix chain 'L' and resid 576 through 580 removed outlier: 3.538A pdb=" N TYR L 580 " --> pdb=" O PRO L 577 " (cutoff:3.500A) Processing helix chain 'L' and resid 586 through 601 removed outlier: 3.910A pdb=" N VAL L 601 " --> pdb=" O MET L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 608 Processing helix chain 'L' and resid 610 through 628 removed outlier: 3.917A pdb=" N ILE L 614 " --> pdb=" O GLN L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 648 removed outlier: 3.709A pdb=" N LEU L 640 " --> pdb=" O LEU L 636 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 655 through 661 removed outlier: 3.570A pdb=" N ARG L 661 " --> pdb=" O ILE L 657 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 684 Processing helix chain 'L' and resid 691 through 705 Processing helix chain 'L' and resid 706 through 708 No H-bonds generated for 'chain 'L' and resid 706 through 708' Processing helix chain 'L' and resid 715 through 735 Proline residue: L 730 - end of helix Processing helix chain 'L' and resid 746 through 761 removed outlier: 3.667A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 1089 through 1096 Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 3.741A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1165 through 1182 removed outlier: 3.741A pdb=" N PHE L1169 " --> pdb=" O ASN L1165 " (cutoff:3.500A) Processing helix chain 'L' and resid 1193 through 1198 Processing helix chain 'L' and resid 1199 through 1210 Processing helix chain 'L' and resid 1219 through 1236 Processing helix chain 'L' and resid 1242 through 1259 Processing helix chain 'L' and resid 1267 through 1278 Processing helix chain 'L' and resid 1297 through 1320 Processing helix chain 'L' and resid 1338 through 1348 Processing helix chain 'L' and resid 1348 through 1366 Processing helix chain 'L' and resid 1396 through 1407 Processing helix chain 'L' and resid 1412 through 1431 Processing helix chain 'L' and resid 1433 through 1451 Processing helix chain 'L' and resid 1465 through 1471 removed outlier: 3.729A pdb=" N TRP L1469 " --> pdb=" O ASP L1465 " (cutoff:3.500A) Processing helix chain 'L' and resid 1473 through 1486 Processing helix chain 'L' and resid 1486 through 1507 removed outlier: 3.631A pdb=" N CYS L1490 " --> pdb=" O ILE L1486 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L1491 " --> pdb=" O PRO L1487 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG L1492 " --> pdb=" O ASP L1488 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE L1493 " --> pdb=" O ALA L1489 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY L1507 " --> pdb=" O LYS L1503 " (cutoff:3.500A) Processing helix chain 'L' and resid 1524 through 1533 removed outlier: 4.025A pdb=" N ASN L1528 " --> pdb=" O SER L1524 " (cutoff:3.500A) Processing helix chain 'L' and resid 1541 through 1543 No H-bonds generated for 'chain 'L' and resid 1541 through 1543' Processing helix chain 'L' and resid 1579 through 1589 Processing helix chain 'L' and resid 1595 through 1608 removed outlier: 4.101A pdb=" N ALA L1608 " --> pdb=" O ILE L1604 " (cutoff:3.500A) Processing helix chain 'L' and resid 1612 through 1626 Processing helix chain 'L' and resid 1638 through 1649 removed outlier: 3.791A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1674 through 1679 removed outlier: 4.408A pdb=" N ILE L1678 " --> pdb=" O ASN L1674 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER L1679 " --> pdb=" O GLU L1675 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1674 through 1679' Processing helix chain 'L' and resid 1684 through 1700 Processing helix chain 'L' and resid 1701 through 1705 Processing helix chain 'L' and resid 1778 through 1790 removed outlier: 4.045A pdb=" N LEU L1782 " --> pdb=" O LYS L1778 " (cutoff:3.500A) Processing helix chain 'L' and resid 1795 through 1800 removed outlier: 3.754A pdb=" N HIS L1798 " --> pdb=" O LEU L1795 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE L1799 " --> pdb=" O VAL L1796 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL L1800 " --> pdb=" O SER L1797 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1795 through 1800' Processing helix chain 'L' and resid 1812 through 1817 Processing sheet with id=AA1, first strand: chain 'L' and resid 61 through 62 removed outlier: 6.465A pdb=" N LEU L 98 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'L' and resid 207 through 208 removed outlier: 6.367A pdb=" N LEU L 207 " --> pdb=" O TYR L1107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 258 through 260 Processing sheet with id=AA5, first strand: chain 'L' and resid 374 through 377 removed outlier: 3.726A pdb=" N ARG L 381 " --> pdb=" O SER L 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 738 through 739 removed outlier: 7.073A pdb=" N PHE L1119 " --> pdb=" O GLU L1240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1381 through 1383 Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 8.925A pdb=" N GLN L1662 " --> pdb=" O LEU L1548 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU L1548 " --> pdb=" O GLN L1662 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 1629 through 1630 Processing sheet with id=AB1, first strand: chain 'L' and resid 1723 through 1726 645 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3356 1.33 - 1.45: 1834 1.45 - 1.57: 6604 1.57 - 1.69: 11 1.69 - 1.81: 107 Bond restraints: 11912 Sorted by residual: bond pdb=" N ILE L 348 " pdb=" CA ILE L 348 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.10e+00 bond pdb=" N VAL L1712 " pdb=" CA VAL L1712 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.76e+00 bond pdb=" N GLN L1333 " pdb=" CA GLN L1333 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.60e+00 bond pdb=" N ASP L1332 " pdb=" CA ASP L1332 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.84e+00 bond pdb=" N ASP L 350 " pdb=" CA ASP L 350 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.24e+00 ... (remaining 11907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 15561 1.38 - 2.75: 431 2.75 - 4.13: 89 4.13 - 5.50: 19 5.50 - 6.88: 2 Bond angle restraints: 16102 Sorted by residual: angle pdb=" N LYS L 602 " pdb=" CA LYS L 602 " pdb=" C LYS L 602 " ideal model delta sigma weight residual 114.62 110.76 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA ASP L1332 " pdb=" C ASP L1332 " pdb=" O ASP L1332 " ideal model delta sigma weight residual 121.56 117.92 3.64 1.09e+00 8.42e-01 1.12e+01 angle pdb=" N ASP L1331 " pdb=" CA ASP L1331 " pdb=" C ASP L1331 " ideal model delta sigma weight residual 114.04 109.94 4.10 1.24e+00 6.50e-01 1.09e+01 angle pdb=" O ILE L 348 " pdb=" C ILE L 348 " pdb=" N PHE L 349 " ideal model delta sigma weight residual 121.91 124.65 -2.74 9.80e-01 1.04e+00 7.80e+00 angle pdb=" CA ILE L 348 " pdb=" C ILE L 348 " pdb=" O ILE L 348 " ideal model delta sigma weight residual 121.17 118.23 2.94 1.06e+00 8.90e-01 7.68e+00 ... (remaining 16097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.21: 6545 18.21 - 36.43: 542 36.43 - 54.64: 101 54.64 - 72.85: 34 72.85 - 91.07: 16 Dihedral angle restraints: 7238 sinusoidal: 3008 harmonic: 4230 Sorted by residual: dihedral pdb=" C4' U E 11 " pdb=" C3' U E 11 " pdb=" C2' U E 11 " pdb=" C1' U E 11 " ideal model delta sinusoidal sigma weight residual 36.34 -36.34 72.68 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' C E 15 " pdb=" C3' C E 15 " pdb=" C2' C E 15 " pdb=" C1' C E 15 " ideal model delta sinusoidal sigma weight residual 36.35 -34.50 70.85 1 3.10e+00 1.04e-01 6.71e+02 dihedral pdb=" C4' U E 13 " pdb=" C3' U E 13 " pdb=" C2' U E 13 " pdb=" C1' U E 13 " ideal model delta sinusoidal sigma weight residual 36.34 -34.20 70.55 1 3.10e+00 1.04e-01 6.66e+02 ... (remaining 7235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1530 0.056 - 0.111: 261 0.111 - 0.167: 30 0.167 - 0.223: 6 0.223 - 0.279: 8 Chirality restraints: 1835 Sorted by residual: chirality pdb=" C2' C E 15 " pdb=" C3' C E 15 " pdb=" O2' C E 15 " pdb=" C1' C E 15 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' U E 11 " pdb=" C3' U E 11 " pdb=" O2' U E 11 " pdb=" C1' U E 11 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C2' U E 13 " pdb=" C3' U E 13 " pdb=" O2' U E 13 " pdb=" C1' U E 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1832 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L1666 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO L1667 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO L1667 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO L1667 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L1486 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO L1487 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO L1487 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L1487 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G E 12 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.06e+00 pdb=" N9 G E 12 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G E 12 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G E 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G E 12 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G E 12 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G E 12 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G E 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G E 12 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G E 12 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G E 12 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G E 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 181 2.68 - 3.23: 11139 3.23 - 3.79: 18525 3.79 - 4.34: 25058 4.34 - 4.90: 41163 Nonbonded interactions: 96066 Sorted by model distance: nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.121 3.040 nonbonded pdb=" O ASN L1586 " pdb=" OG SER L1590 " model vdw 2.164 3.040 nonbonded pdb=" NH2 ARG L1452 " pdb=" OP1 U E 13 " model vdw 2.181 3.120 nonbonded pdb=" OD2 ASP L1332 " pdb=" N LYS L1384 " model vdw 2.212 3.120 nonbonded pdb=" OG SER L1626 " pdb=" O2' U E 11 " model vdw 2.225 3.040 ... (remaining 96061 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.430 Find NCS groups from input model: 0.060 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: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11915 Z= 0.185 Angle : 0.575 6.880 16102 Z= 0.316 Chirality : 0.046 0.279 1835 Planarity : 0.004 0.077 2015 Dihedral : 14.763 91.066 4484 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.74 % Rotamer: Outliers : 0.53 % Allowed : 0.30 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1413 helix: 1.77 (0.18), residues: 797 sheet: -0.13 (0.51), residues: 101 loop : -1.06 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L1347 TYR 0.013 0.001 TYR L1187 PHE 0.015 0.002 PHE L 539 TRP 0.013 0.002 TRP L1547 HIS 0.004 0.001 HIS L1522 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (11912) covalent geometry : angle 0.57502 / 0.32 (16102) hydrogen bonds : bond 0.13112 / 8.30 ( 645) hydrogen bonds : angle 5.25496 / 3.72 ( 1851) metal coordination : bond 0.00147 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 165 PHE cc_start: 0.7704 (t80) cc_final: 0.7197 (t80) outliers start: 7 outliers final: 1 residues processed: 172 average time/residue: 0.1399 time to fit residues: 32.1900 Evaluate side-chains 89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 341 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 175 ASN L 359 HIS L 506 ASN L 720 GLN L1105 GLN L1171 ASN ** L1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1346 GLN L1481 GLN L1516 ASN L1554 HIS L1789 ASN L1798 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.056733 restraints weight = 60556.164| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.60 r_work: 0.2931 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11915 Z= 0.134 Angle : 0.619 13.481 16102 Z= 0.300 Chirality : 0.049 0.673 1835 Planarity : 0.004 0.064 2015 Dihedral : 6.170 142.734 1616 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 0.61 % Allowed : 4.94 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1413 helix: 2.02 (0.18), residues: 807 sheet: 0.00 (0.52), residues: 94 loop : -0.93 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 398 TYR 0.012 0.001 TYR L 15 PHE 0.018 0.001 PHE L 539 TRP 0.011 0.001 TRP L1194 HIS 0.007 0.001 HIS L1798 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11912) covalent geometry : angle 0.61887 / 0.30 (16102) hydrogen bonds : bond 0.04113 / 2.68 ( 645) hydrogen bonds : angle 4.15061 / 2.95 ( 1851) metal coordination : bond 0.00078 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8087 (mp0) REVERT: L 363 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8432 (ttp80) REVERT: L 365 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8281 (mmmt) REVERT: L 368 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8680 (mtmm) REVERT: L 1197 MET cc_start: 0.8959 (mmt) cc_final: 0.8742 (mmt) outliers start: 8 outliers final: 5 residues processed: 95 average time/residue: 0.1226 time to fit residues: 16.5036 Evaluate side-chains 87 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 138 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.4661 > 50:) chunk 18 optimal weight: 0.6980 chunk 114 optimal weight: 0.0870 chunk 123 optimal weight: 6.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 175 ASN L 324 GLN L1522 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.074798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057620 restraints weight = 62226.879| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.64 r_work: 0.2958 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11915 Z= 0.106 Angle : 0.537 10.018 16102 Z= 0.266 Chirality : 0.042 0.396 1835 Planarity : 0.004 0.058 2015 Dihedral : 6.203 133.250 1616 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 0.61 % Allowed : 5.93 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.23), residues: 1413 helix: 2.23 (0.18), residues: 806 sheet: 0.31 (0.54), residues: 87 loop : -0.95 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 300 TYR 0.024 0.001 TYR L 15 PHE 0.018 0.001 PHE L 165 TRP 0.016 0.001 TRP L1194 HIS 0.003 0.000 HIS L 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11912) covalent geometry : angle 0.53729 / 0.27 (16102) hydrogen bonds : bond 0.03430 / 2.22 ( 645) hydrogen bonds : angle 3.87125 / 2.76 ( 1851) metal coordination : bond 0.00066 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8059 (mp0) REVERT: L 363 ARG cc_start: 0.8764 (ttp80) cc_final: 0.8326 (ttp80) REVERT: L 415 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8669 (mp10) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.1282 time to fit residues: 17.9501 Evaluate side-chains 85 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 14 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 79 optimal weight: 0.0270 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 91 optimal weight: 0.0050 chunk 65 optimal weight: 4.9990 chunk 119 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.075052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058724 restraints weight = 42735.664| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.98 r_work: 0.3002 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11915 Z= 0.096 Angle : 0.525 10.073 16102 Z= 0.256 Chirality : 0.041 0.372 1835 Planarity : 0.004 0.054 2015 Dihedral : 6.076 132.625 1615 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.76 % Allowed : 7.83 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.23), residues: 1413 helix: 2.28 (0.18), residues: 809 sheet: 0.18 (0.54), residues: 87 loop : -0.90 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 398 TYR 0.014 0.001 TYR L 15 PHE 0.018 0.001 PHE L 539 TRP 0.009 0.001 TRP L1194 HIS 0.002 0.000 HIS L1359 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (11912) covalent geometry : angle 0.52515 / 0.26 (16102) hydrogen bonds : bond 0.03235 / 2.10 ( 645) hydrogen bonds : angle 3.81988 / 2.72 ( 1851) metal coordination : bond 0.00062 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: L 363 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8280 (ttp80) REVERT: L 415 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8639 (mp10) REVERT: L 1197 MET cc_start: 0.8999 (mmt) cc_final: 0.8794 (mmt) REVERT: L 1345 MET cc_start: 0.8823 (ttp) cc_final: 0.8559 (ttm) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1359 time to fit residues: 17.0542 Evaluate side-chains 87 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 0.0050 chunk 110 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 62 HIS ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.072550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055327 restraints weight = 62422.060| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.63 r_work: 0.2903 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11915 Z= 0.148 Angle : 0.544 10.418 16102 Z= 0.268 Chirality : 0.042 0.320 1835 Planarity : 0.004 0.052 2015 Dihedral : 6.439 135.283 1615 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.84 % Allowed : 8.43 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.23), residues: 1413 helix: 2.29 (0.18), residues: 808 sheet: -0.08 (0.51), residues: 96 loop : -0.95 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 398 TYR 0.012 0.001 TYR L1450 PHE 0.015 0.001 PHE L 539 TRP 0.008 0.001 TRP L1194 HIS 0.003 0.001 HIS L 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (11912) covalent geometry : angle 0.54381 / 0.27 (16102) hydrogen bonds : bond 0.03620 / 2.34 ( 645) hydrogen bonds : angle 3.91678 / 2.79 ( 1851) metal coordination : bond 0.00148 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8030 (mp0) REVERT: L 415 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8702 (mp10) REVERT: L 446 MET cc_start: 0.9379 (mmm) cc_final: 0.8998 (mmt) REVERT: L 473 ARG cc_start: 0.5724 (tpp-160) cc_final: 0.5458 (tpp-160) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.1301 time to fit residues: 16.1434 Evaluate side-chains 89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 463 SER Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 129 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053184 restraints weight = 71769.955| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.92 r_work: 0.2838 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11915 Z= 0.201 Angle : 0.585 9.903 16102 Z= 0.291 Chirality : 0.045 0.424 1835 Planarity : 0.004 0.050 2015 Dihedral : 6.573 136.303 1615 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.76 % Allowed : 8.89 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.23), residues: 1413 helix: 2.12 (0.18), residues: 808 sheet: -0.30 (0.51), residues: 98 loop : -1.04 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 398 TYR 0.011 0.001 TYR L1388 PHE 0.015 0.002 PHE L 539 TRP 0.013 0.002 TRP L1194 HIS 0.003 0.001 HIS L 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (11912) covalent geometry : angle 0.58543 / 0.29 (16102) hydrogen bonds : bond 0.04028 / 2.60 ( 645) hydrogen bonds : angle 4.11046 / 2.92 ( 1851) metal coordination : bond 0.00204 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: L 363 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8301 (ttp80) REVERT: L 415 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8702 (mp10) REVERT: L 1197 MET cc_start: 0.9003 (mmt) cc_final: 0.8774 (mmt) REVERT: L 1345 MET cc_start: 0.8960 (ttp) cc_final: 0.8682 (ttm) REVERT: L 1672 ASP cc_start: 0.8688 (m-30) cc_final: 0.8455 (t70) outliers start: 10 outliers final: 9 residues processed: 91 average time/residue: 0.1323 time to fit residues: 16.7475 Evaluate side-chains 89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 463 SER Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054786 restraints weight = 66569.096| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.75 r_work: 0.2893 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11915 Z= 0.107 Angle : 0.518 10.320 16102 Z= 0.257 Chirality : 0.041 0.290 1835 Planarity : 0.004 0.048 2015 Dihedral : 6.458 134.286 1615 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.68 % Allowed : 8.89 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.23), residues: 1413 helix: 2.25 (0.18), residues: 806 sheet: -0.00 (0.57), residues: 82 loop : -0.98 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.010 0.001 TYR L 15 PHE 0.015 0.001 PHE L 539 TRP 0.011 0.001 TRP L1194 HIS 0.002 0.000 HIS L1359 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11912) covalent geometry : angle 0.51850 / 0.26 (16102) hydrogen bonds : bond 0.03456 / 2.25 ( 645) hydrogen bonds : angle 3.92480 / 2.80 ( 1851) metal coordination : bond 0.00075 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: L 363 ARG cc_start: 0.8545 (ttp80) cc_final: 0.8309 (ttp80) REVERT: L 415 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8683 (mp10) REVERT: L 1197 MET cc_start: 0.8997 (mmt) cc_final: 0.8769 (mmt) REVERT: L 1345 MET cc_start: 0.8891 (ttp) cc_final: 0.8616 (ttm) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.1293 time to fit residues: 16.9902 Evaluate side-chains 85 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 463 SER Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 36 optimal weight: 0.0570 chunk 117 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055650 restraints weight = 70686.211| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.89 r_work: 0.2914 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11915 Z= 0.099 Angle : 0.507 10.671 16102 Z= 0.250 Chirality : 0.041 0.278 1835 Planarity : 0.003 0.048 2015 Dihedral : 6.316 133.191 1615 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.61 % Allowed : 9.12 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.23), residues: 1413 helix: 2.31 (0.18), residues: 810 sheet: -0.05 (0.56), residues: 84 loop : -0.93 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 24 TYR 0.018 0.001 TYR L 15 PHE 0.023 0.001 PHE L 165 TRP 0.011 0.001 TRP L1194 HIS 0.002 0.000 HIS L1359 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (11912) covalent geometry : angle 0.50696 / 0.25 (16102) hydrogen bonds : bond 0.03183 / 2.06 ( 645) hydrogen bonds : angle 3.80603 / 2.72 ( 1851) metal coordination : bond 0.00086 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: L 363 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8296 (ttp80) REVERT: L 415 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8695 (mp10) REVERT: L 1197 MET cc_start: 0.8974 (mmt) cc_final: 0.8727 (mmt) REVERT: L 1345 MET cc_start: 0.8858 (ttp) cc_final: 0.8573 (ttm) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.1413 time to fit residues: 18.1675 Evaluate side-chains 86 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 463 SER Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 chunk 77 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.073104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057376 restraints weight = 36133.728| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.67 r_work: 0.2987 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11915 Z= 0.098 Angle : 0.507 10.599 16102 Z= 0.251 Chirality : 0.040 0.272 1835 Planarity : 0.003 0.047 2015 Dihedral : 6.273 133.245 1615 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.46 % Allowed : 9.42 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1413 helix: 2.34 (0.18), residues: 811 sheet: 0.01 (0.57), residues: 84 loop : -0.89 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 398 TYR 0.014 0.001 TYR L 15 PHE 0.020 0.001 PHE L 165 TRP 0.010 0.001 TRP L1194 HIS 0.002 0.000 HIS L1359 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (11912) covalent geometry : angle 0.50722 / 0.25 (16102) hydrogen bonds : bond 0.03152 / 2.06 ( 645) hydrogen bonds : angle 3.77579 / 2.69 ( 1851) metal coordination : bond 0.00074 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: L 363 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8288 (ttp80) REVERT: L 415 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8641 (mp10) REVERT: L 1197 MET cc_start: 0.8934 (mmt) cc_final: 0.8668 (mmt) REVERT: L 1345 MET cc_start: 0.8821 (ttp) cc_final: 0.8536 (ttm) outliers start: 6 outliers final: 6 residues processed: 90 average time/residue: 0.1321 time to fit residues: 16.8387 Evaluate side-chains 89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 463 SER Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 70 optimal weight: 0.4980 chunk 7 optimal weight: 0.0070 chunk 104 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 141 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.073302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056629 restraints weight = 57886.122| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.46 r_work: 0.2952 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11915 Z= 0.096 Angle : 0.511 10.512 16102 Z= 0.252 Chirality : 0.040 0.262 1835 Planarity : 0.003 0.047 2015 Dihedral : 6.220 133.017 1615 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.53 % Allowed : 9.65 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.23), residues: 1413 helix: 2.36 (0.18), residues: 811 sheet: 0.01 (0.57), residues: 84 loop : -0.89 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 398 TYR 0.016 0.001 TYR L 15 PHE 0.018 0.001 PHE L 165 TRP 0.010 0.001 TRP L1194 HIS 0.002 0.000 HIS L1359 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (11912) covalent geometry : angle 0.51109 / 0.25 (16102) hydrogen bonds : bond 0.03069 / 2.00 ( 645) hydrogen bonds : angle 3.73271 / 2.66 ( 1851) metal coordination : bond 0.00065 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: L 363 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8316 (ttp80) REVERT: L 415 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8659 (mp10) REVERT: L 691 MET cc_start: 0.8957 (mtp) cc_final: 0.8717 (mtm) REVERT: L 1197 MET cc_start: 0.8964 (mmt) cc_final: 0.8698 (mmt) REVERT: L 1345 MET cc_start: 0.8823 (ttp) cc_final: 0.8550 (ttm) outliers start: 7 outliers final: 7 residues processed: 91 average time/residue: 0.1261 time to fit residues: 16.1273 Evaluate side-chains 91 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 388 THR Chi-restraints excluded: chain L residue 463 SER Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1817 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 0.0060 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.073182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057337 restraints weight = 41187.739| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.86 r_work: 0.2986 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11915 Z= 0.097 Angle : 0.507 10.516 16102 Z= 0.249 Chirality : 0.040 0.262 1835 Planarity : 0.003 0.047 2015 Dihedral : 6.208 133.250 1615 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.53 % Allowed : 9.73 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.23), residues: 1413 helix: 2.39 (0.18), residues: 811 sheet: -0.03 (0.59), residues: 82 loop : -0.90 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 24 TYR 0.015 0.001 TYR L 15 PHE 0.013 0.001 PHE L 539 TRP 0.010 0.001 TRP L1194 HIS 0.002 0.000 HIS L1359 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (11912) covalent geometry : angle 0.50715 / 0.25 (16102) hydrogen bonds : bond 0.03065 / 2.00 ( 645) hydrogen bonds : angle 3.72319 / 2.65 ( 1851) metal coordination : bond 0.00096 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3057.87 seconds wall clock time: 53 minutes 20.37 seconds (3200.37 seconds total)