Starting phenix.real_space_refine on Fri Jul 3 04:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oeb_12863/07_2026/7oeb_12863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oeb_12863/07_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_12863/07_2026/7oeb_12863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_2026/7oeb_12863.map" model { file = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_2026/7oeb_12863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_2026/7oeb_12863.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_2026/7oeb_12863.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oeb_12863/07_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-dev-6108/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: {'RNA': 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: 4.85, per 1000 atoms: 0.42 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 996.7 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: 0.50 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: 2.71 Time building geometry restraints manager: 1.28 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: 15592 1.38 - 2.75: 419 2.75 - 4.13: 75 4.13 - 5.50: 14 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: 6565 18.21 - 36.43: 535 36.43 - 54.64: 98 54.64 - 72.85: 24 72.85 - 91.07: 16 Dihedral angle restraints: 7238 sinusoidal: 3008 harmonic: 4230 Sorted by residual: dihedral pdb=" CA ILE L1670 " pdb=" C ILE L1670 " pdb=" N ARG L1671 " pdb=" CA ARG L1671 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA VAL L 275 " pdb=" C VAL L 275 " pdb=" N ASP L 276 " pdb=" CA ASP L 276 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA MET L1198 " pdb=" C MET L1198 " pdb=" N CYS L1199 " pdb=" CA CYS L1199 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 7235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1217 0.036 - 0.071: 452 0.071 - 0.107: 123 0.107 - 0.143: 34 0.143 - 0.179: 9 Chirality restraints: 1835 Sorted by residual: chirality pdb=" CB ILE L 138 " pdb=" CA ILE L 138 " pdb=" CG1 ILE L 138 " pdb=" CG2 ILE L 138 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA VAL L1712 " pdb=" N VAL L1712 " pdb=" C VAL L1712 " pdb=" CB VAL L1712 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA ILE L1376 " pdb=" N ILE L1376 " pdb=" C ILE L1376 " pdb=" CB ILE L1376 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 ... (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: 2.290 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 17.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- 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= 0.184 Angle : 0.557 6.880 16102 Z= 0.313 Chirality : 0.042 0.179 1835 Planarity : 0.004 0.077 2015 Dihedral : 14.394 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 0.00359 / 0.18 (11912) covalent geometry : angle 0.55750 / 0.31 (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 : 0.482 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: 0.1511 time to fit residues: 34.4998 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 : 0.373 ------------------------------------------------------------------------------- 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 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 = 0.3516 r_free = 0.3516 target = 0.073834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056640 restraints weight = 60583.383| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.59 r_work: 0.2927 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 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 = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11915 Z= 0.128 Angle : 0.549 9.351 16102 Z= 0.282 Chirality : 0.040 0.153 1835 Planarity : 0.004 0.064 2015 Dihedral : 5.006 68.151 1616 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 0.53 % Allowed : 5.09 % Favored : 94.38 % 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: 1.26 (0.23), residues: 1413 helix: 2.02 (0.18), residues: 807 sheet: 0.17 (0.54), residues: 89 loop : -0.97 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 398 TYR 0.015 0.001 TYR L 15 PHE 0.017 0.001 PHE L1716 TRP 0.013 0.001 TRP L1194 HIS 0.008 0.001 HIS L1798 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11912) covalent geometry : angle 0.54877 / 0.28 (16102) hydrogen bonds : bond 0.03999 / 2.61 ( 645) hydrogen bonds : angle 4.12093 / 2.92 ( 1851) metal coordination : bond 0.00106 / 0.06 ( 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: 7 poor density : 92 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8096 (mp0) REVERT: L 363 ARG cc_start: 0.8863 (ttp80) cc_final: 0.8448 (ttp80) REVERT: L 365 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8280 (mmmt) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.1245 time to fit residues: 16.7861 Evaluate side-chains 87 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 1817 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 4 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 0.0970 chunk 123 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 125 GLN L 175 ASN L1522 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057185 restraints weight = 62501.037| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.63 r_work: 0.2950 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 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 = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2009 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 : 0.498 9.757 16102 Z= 0.255 Chirality : 0.038 0.152 1835 Planarity : 0.004 0.058 2015 Dihedral : 4.808 66.544 1615 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 0.76 % Allowed : 6.31 % Favored : 92.93 % 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: 2.22 (0.18), residues: 806 sheet: 0.11 (0.53), residues: 92 loop : -0.90 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 398 TYR 0.024 0.001 TYR L 15 PHE 0.012 0.001 PHE L 539 TRP 0.014 0.001 TRP L1194 HIS 0.003 0.000 HIS L 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (11912) covalent geometry : angle 0.49790 / 0.26 (16102) hydrogen bonds : bond 0.03482 / 2.25 ( 645) hydrogen bonds : angle 3.90852 / 2.79 ( 1851) metal coordination : bond 0.00080 / 0.04 ( 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 102 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8058 (mp0) REVERT: L 363 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8320 (ttp80) REVERT: L 415 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8673 (mp10) REVERT: L 691 MET cc_start: 0.8862 (mtp) cc_final: 0.8600 (mtm) REVERT: L 1197 MET cc_start: 0.9026 (mmt) cc_final: 0.8822 (mmt) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.1253 time to fit residues: 17.5557 Evaluate side-chains 86 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 125 GLN 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: 5.9990 chunk 113 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.072788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056512 restraints weight = 42184.424| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.93 r_work: 0.2952 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 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: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2096 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= 0.144 Angle : 0.512 9.817 16102 Z= 0.261 Chirality : 0.040 0.182 1835 Planarity : 0.004 0.054 2015 Dihedral : 4.814 66.303 1615 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.61 % Allowed : 8.13 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.23), residues: 1413 helix: 2.22 (0.18), residues: 806 sheet: -0.06 (0.52), residues: 96 loop : -0.96 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 398 TYR 0.016 0.001 TYR L 15 PHE 0.014 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 0.00332 / 0.14 (11912) covalent geometry : angle 0.51152 / 0.26 (16102) hydrogen bonds : bond 0.03631 / 2.35 ( 645) hydrogen bonds : angle 3.95513 / 2.82 ( 1851) metal coordination : bond 0.00135 / 0.07 ( 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 91 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7992 (mp0) REVERT: L 363 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8275 (ttp80) REVERT: L 415 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8626 (mp10) REVERT: L 483 MET cc_start: 0.8349 (mmt) cc_final: 0.8076 (mmt) REVERT: L 691 MET cc_start: 0.8843 (mtp) cc_final: 0.8577 (mtm) REVERT: L 1197 MET cc_start: 0.9019 (mmt) cc_final: 0.8818 (mmt) REVERT: L 1505 LYS cc_start: 0.8296 (mttt) cc_final: 0.8081 (ttmt) outliers start: 8 outliers final: 8 residues processed: 89 average time/residue: 0.1403 time to fit residues: 17.3112 Evaluate side-chains 87 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 1817 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 0.0670 chunk 110 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 93 optimal weight: 6.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.073110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056103 restraints weight = 62309.397| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.61 r_work: 0.2922 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 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 = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11915 Z= 0.110 Angle : 0.481 10.492 16102 Z= 0.244 Chirality : 0.038 0.186 1835 Planarity : 0.004 0.051 2015 Dihedral : 4.719 65.274 1615 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.76 % Allowed : 8.43 % Favored : 90.81 % 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: 2.31 (0.18), residues: 806 sheet: -0.23 (0.53), residues: 92 loop : -0.92 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 398 TYR 0.014 0.001 TYR L 15 PHE 0.015 0.001 PHE L 539 TRP 0.006 0.001 TRP L1194 HIS 0.002 0.000 HIS L1359 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11912) covalent geometry : angle 0.48119 / 0.24 (16102) hydrogen bonds : bond 0.03313 / 2.15 ( 645) hydrogen bonds : angle 3.84655 / 2.74 ( 1851) metal coordination : bond 0.00108 / 0.06 ( 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: 10 poor density : 83 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8013 (mp0) REVERT: L 415 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8684 (mp10) REVERT: L 473 ARG cc_start: 0.5711 (tpp-160) cc_final: 0.5435 (tpp-160) REVERT: L 483 MET cc_start: 0.8305 (mmt) cc_final: 0.8064 (mmt) REVERT: L 691 MET cc_start: 0.8900 (mtp) cc_final: 0.8651 (mtm) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1525 time to fit residues: 18.8064 Evaluate side-chains 87 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 1817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 129 optimal weight: 0.0370 chunk 134 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.056275 restraints weight = 71319.736| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.88 r_work: 0.2925 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 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 = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2443 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= 0.095 Angle : 0.469 10.652 16102 Z= 0.236 Chirality : 0.038 0.174 1835 Planarity : 0.003 0.050 2015 Dihedral : 4.633 64.204 1615 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.68 % Allowed : 8.81 % Favored : 90.50 % 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: 1.64 (0.23), residues: 1413 helix: 2.38 (0.18), residues: 809 sheet: 0.07 (0.55), residues: 84 loop : -0.88 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 398 TYR 0.014 0.001 TYR L 15 PHE 0.014 0.001 PHE L 539 TRP 0.014 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 0.46883 / 0.24 (16102) hydrogen bonds : bond 0.03121 / 2.03 ( 645) hydrogen bonds : angle 3.77482 / 2.69 ( 1851) metal coordination : bond 0.00081 / 0.04 ( 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 104 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7981 (mp0) REVERT: L 169 ARG cc_start: 0.8720 (mtm180) cc_final: 0.8235 (mtm110) REVERT: L 192 MET cc_start: 0.7351 (mtt) cc_final: 0.6899 (mtt) REVERT: L 363 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8298 (ttp80) REVERT: L 415 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8685 (mp10) REVERT: L 691 MET cc_start: 0.8904 (mtp) cc_final: 0.8659 (mtm) REVERT: L 1345 MET cc_start: 0.8848 (ttp) cc_final: 0.8562 (ttm) outliers start: 9 outliers final: 7 residues processed: 100 average time/residue: 0.1439 time to fit residues: 19.7140 Evaluate side-chains 90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 1292 MET Chi-restraints excluded: chain L residue 1298 HIS 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: 5.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 62 HIS ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1554 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.071149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053829 restraints weight = 66798.314| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.78 r_work: 0.2865 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11915 Z= 0.181 Angle : 0.533 10.344 16102 Z= 0.272 Chirality : 0.040 0.197 1835 Planarity : 0.004 0.049 2015 Dihedral : 4.860 65.450 1615 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.68 % Allowed : 8.43 % Favored : 90.88 % 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: 1.43 (0.23), residues: 1413 helix: 2.27 (0.18), residues: 808 sheet: -0.33 (0.51), residues: 98 loop : -1.01 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.018 0.001 TYR L 15 PHE 0.014 0.001 PHE L 539 TRP 0.008 0.001 TRP L1547 HIS 0.003 0.001 HIS L 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (11912) covalent geometry : angle 0.53310 / 0.27 (16102) hydrogen bonds : bond 0.03785 / 2.44 ( 645) hydrogen bonds : angle 3.99198 / 2.84 ( 1851) metal coordination : bond 0.00182 / 0.10 ( 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 94 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7986 (mp0) REVERT: L 165 PHE cc_start: 0.9245 (t80) cc_final: 0.8623 (t80) REVERT: L 363 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8292 (ttp80) REVERT: L 415 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8725 (mp10) REVERT: L 691 MET cc_start: 0.8936 (mtp) cc_final: 0.8700 (mtm) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.1472 time to fit residues: 18.4377 Evaluate side-chains 90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 1092 MET 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: 0.1980 chunk 36 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.071995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054891 restraints weight = 70690.964| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.81 r_work: 0.2893 rms_B_bonded: 4.23 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 = 0.42 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 = 0.43 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: 0.8866 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11915 Z= 0.118 Angle : 0.493 10.564 16102 Z= 0.250 Chirality : 0.039 0.179 1835 Planarity : 0.004 0.048 2015 Dihedral : 4.783 64.800 1615 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.68 % Allowed : 8.81 % Favored : 90.50 % 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: 1.50 (0.23), residues: 1413 helix: 2.29 (0.18), residues: 810 sheet: -0.01 (0.57), residues: 82 loop : -0.97 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.017 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 0.00269 / 0.12 (11912) covalent geometry : angle 0.49286 / 0.25 (16102) hydrogen bonds : bond 0.03359 / 2.18 ( 645) hydrogen bonds : angle 3.87966 / 2.76 ( 1851) metal coordination : bond 0.00102 / 0.05 ( 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 93 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7939 (mp0) REVERT: L 363 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8303 (ttp80) REVERT: L 415 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8699 (mp10) REVERT: L 691 MET cc_start: 0.8899 (mtp) cc_final: 0.8645 (mtm) REVERT: L 1345 MET cc_start: 0.8900 (ttp) cc_final: 0.8615 (ttm) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.1241 time to fit residues: 16.1752 Evaluate side-chains 89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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: 0.7980 chunk 109 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.072497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056887 restraints weight = 36092.356| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.63 r_work: 0.2974 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 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 = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11915 Z= 0.107 Angle : 0.482 10.636 16102 Z= 0.245 Chirality : 0.038 0.184 1835 Planarity : 0.004 0.048 2015 Dihedral : 4.693 63.338 1615 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.53 % Allowed : 8.81 % Favored : 90.65 % 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: 1.57 (0.23), residues: 1413 helix: 2.36 (0.18), residues: 809 sheet: -0.00 (0.58), residues: 82 loop : -0.95 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.017 0.001 TYR L 15 PHE 0.014 0.001 PHE L 539 TRP 0.010 0.001 TRP L1194 HIS 0.002 0.000 HIS L 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11912) covalent geometry : angle 0.48241 / 0.24 (16102) hydrogen bonds : bond 0.03216 / 2.09 ( 645) hydrogen bonds : angle 3.79353 / 2.70 ( 1851) metal coordination : bond 0.00093 / 0.05 ( 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 94 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 150 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7888 (mp0) REVERT: L 363 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8270 (ttp80) REVERT: L 415 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8652 (mp10) REVERT: L 691 MET cc_start: 0.8834 (mtp) cc_final: 0.8609 (mtm) REVERT: L 1345 MET cc_start: 0.8853 (ttp) cc_final: 0.8564 (ttm) outliers start: 7 outliers final: 7 residues processed: 93 average time/residue: 0.1291 time to fit residues: 17.0070 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 : 0.467 ------------------------------------------------------------------------------- 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 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.0020 chunk 10 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.071872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055170 restraints weight = 57976.749| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.43 r_work: 0.2912 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11915 Z= 0.124 Angle : 0.497 10.432 16102 Z= 0.251 Chirality : 0.039 0.189 1835 Planarity : 0.004 0.047 2015 Dihedral : 4.716 63.526 1615 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.53 % Allowed : 9.04 % 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: 1.54 (0.23), residues: 1413 helix: 2.35 (0.18), residues: 808 sheet: -0.06 (0.56), residues: 88 loop : -1.00 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.017 0.001 TYR L 15 PHE 0.013 0.001 PHE L 539 TRP 0.009 0.001 TRP L1194 HIS 0.002 0.001 HIS L1184 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11912) covalent geometry : angle 0.49672 / 0.25 (16102) hydrogen bonds : bond 0.03367 / 2.19 ( 645) hydrogen bonds : angle 3.83593 / 2.73 ( 1851) metal coordination : bond 0.00113 / 0.06 ( 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 91 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.5965 (tmm) cc_final: 0.5714 (tmm) REVERT: L 150 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7917 (mp0) REVERT: L 363 ARG cc_start: 0.8545 (ttp80) cc_final: 0.8307 (ttp80) REVERT: L 415 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8696 (mp10) REVERT: L 691 MET cc_start: 0.8888 (mtp) cc_final: 0.8668 (mtm) REVERT: L 1345 MET cc_start: 0.8880 (ttp) cc_final: 0.8601 (ttm) outliers start: 7 outliers final: 7 residues processed: 90 average time/residue: 0.1283 time to fit residues: 16.1787 Evaluate side-chains 90 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 0.5980 chunk 69 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.072018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056107 restraints weight = 41071.003| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.84 r_work: 0.2948 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11915 Z= 0.114 Angle : 0.490 10.334 16102 Z= 0.248 Chirality : 0.039 0.216 1835 Planarity : 0.004 0.047 2015 Dihedral : 4.726 63.463 1615 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.53 % Allowed : 9.19 % 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: 1.53 (0.23), residues: 1413 helix: 2.34 (0.18), residues: 808 sheet: -0.05 (0.58), residues: 82 loop : -0.98 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.018 0.001 TYR L 15 PHE 0.020 0.001 PHE L 165 TRP 0.009 0.001 TRP L1194 HIS 0.002 0.000 HIS L 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (11912) covalent geometry : angle 0.49035 / 0.25 (16102) hydrogen bonds : bond 0.03318 / 2.17 ( 645) hydrogen bonds : angle 3.82920 / 2.73 ( 1851) metal coordination : bond 0.00095 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2935.20 seconds wall clock time: 51 minutes 14.08 seconds (3074.08 seconds total)