Starting phenix.real_space_refine on Fri Jul 3 04:18:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2026/7oea_12862.map" } resolution = 2.7 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 7 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 7426 2.51 5 N 1968 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 11703 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 11535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1432, 11525 Classifications: {'peptide': 1432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1385} 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: 1432, 11525 Classifications: {'peptide': 1432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1385} 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: 11731 Chain: "E" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 3} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2, 'water': 11} Link IDs: {None: 12} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2475 SG CYS L 321 37.569 99.999 65.452 1.00 57.95 S ATOM 2852 SG CYS L 366 37.387 99.892 68.968 1.00 69.67 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: 3.54, per 1000 atoms: 0.30 Number of scatterers: 11703 At special positions: 0 Unit cell: (117.434, 132.32, 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 71 16.00 P 7 15.00 Mg 1 11.99 O 2229 8.00 N 1968 7.00 C 7426 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: 0.74 Conformation dependent library (CDL) restraints added in 649.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2750 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 10 sheets defined 59.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 19 through 32 removed outlier: 4.060A pdb=" N ARG L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 3.801A 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 200 through 206 removed outlier: 3.720A pdb=" N LEU L 203 " --> pdb=" O VAL L 200 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL L 205 " --> pdb=" O SER L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 223 removed outlier: 3.777A 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 284 through 293 Processing helix chain 'L' and resid 296 through 303 Processing helix chain 'L' and resid 321 through 334 removed outlier: 3.510A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 365 Processing helix chain 'L' and resid 385 through 404 Processing helix chain 'L' and resid 412 through 434 Processing helix chain 'L' and resid 438 through 443 Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.630A 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 Processing helix chain 'L' and resid 586 through 601 removed outlier: 3.760A pdb=" N VAL L 601 " --> pdb=" O MET L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 608 through 610 No H-bonds generated for 'chain 'L' and resid 608 through 610' Processing helix chain 'L' and resid 611 through 628 Processing helix chain 'L' and resid 630 through 648 removed outlier: 3.624A pdb=" N LEU L 640 " --> pdb=" O LEU L 636 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 655 through 660 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 709 Processing helix chain 'L' and resid 715 through 735 Proline residue: L 730 - end of helix Processing helix chain 'L' and resid 746 through 762 removed outlier: 3.627A 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 1090 through 1096 Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 4.015A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1166 through 1182 Processing helix chain 'L' and resid 1193 through 1198 Processing helix chain 'L' and resid 1199 through 1210 removed outlier: 3.521A pdb=" N ASN L1209 " --> pdb=" O ALA L1205 " (cutoff:3.500A) 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 1279 removed outlier: 3.535A pdb=" N ILE L1279 " --> pdb=" O SER L1275 " (cutoff:3.500A) 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 1406 Processing helix chain 'L' and resid 1412 through 1431 Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 3.509A pdb=" N ALA L1451 " --> pdb=" O LEU L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1465 through 1471 removed outlier: 3.697A 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 1490 through 1506 Processing helix chain 'L' and resid 1524 through 1533 removed outlier: 3.650A pdb=" N ASN L1528 " --> pdb=" O SER L1524 " (cutoff:3.500A) Processing helix chain 'L' and resid 1539 through 1544 removed outlier: 3.645A pdb=" N GLU L1544 " --> pdb=" O GLU L1540 " (cutoff:3.500A) Processing helix chain 'L' and resid 1579 through 1589 Processing helix chain 'L' and resid 1595 through 1608 removed outlier: 3.576A pdb=" N LYS L1606 " --> pdb=" O GLU L1602 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.647A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1674 through 1679 removed outlier: 4.051A pdb=" N ILE L1678 " --> pdb=" O ASN L1674 " (cutoff:3.500A) removed outlier: 3.757A 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 1788 removed outlier: 3.952A pdb=" N LEU L1782 " --> pdb=" O LYS L1778 " (cutoff:3.500A) Processing helix chain 'L' and resid 1796 through 1800 removed outlier: 4.012A pdb=" N ILE L1799 " --> pdb=" O VAL L1796 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL L1800 " --> pdb=" O SER L1797 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1796 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: 6.881A 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 removed outlier: 6.674A pdb=" N PHE L 104 " --> pdb=" O ARG L 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 207 through 208 removed outlier: 6.555A pdb=" N LEU L 207 " --> pdb=" O TYR L1107 " (cutoff:3.500A) 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 376 Processing sheet with id=AA6, first strand: chain 'L' and resid 738 through 739 removed outlier: 7.090A pdb=" N PHE L1119 " --> pdb=" O GLU L1240 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY L1129 " --> pdb=" O GLN L1126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1380 through 1382 Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 8.927A pdb=" N GLN L1662 " --> pdb=" O LEU L1548 " (cutoff:3.500A) removed outlier: 5.537A 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 641 hydrogen bonds defined for protein. 1845 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: 1.90 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3566 1.34 - 1.45: 1695 1.45 - 1.57: 6540 1.57 - 1.69: 14 1.69 - 1.81: 105 Bond restraints: 11920 Sorted by residual: bond pdb=" N PRO L1487 " pdb=" CA PRO L1487 " ideal model delta sigma weight residual 1.469 1.699 -0.230 1.28e-02 6.10e+03 3.23e+02 bond pdb=" C ILE L1486 " pdb=" N PRO L1487 " ideal model delta sigma weight residual 1.334 1.451 -0.117 2.34e-02 1.83e+03 2.52e+01 bond pdb=" N PRO L 582 " pdb=" CD PRO L 582 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" N ILE L1408 " pdb=" CA ILE L1408 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.22e-02 6.72e+03 7.93e+00 bond pdb=" N VAL L1401 " pdb=" CA VAL L1401 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.83e+00 ... (remaining 11915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.22: 16113 10.22 - 20.44: 1 20.44 - 30.65: 2 30.65 - 40.87: 1 40.87 - 51.09: 1 Bond angle restraints: 16118 Sorted by residual: angle pdb=" C LEU L1713 " pdb=" CA LEU L1713 " pdb=" CB LEU L1713 " ideal model delta sigma weight residual 110.42 161.51 -51.09 1.99e+00 2.53e-01 6.59e+02 angle pdb=" N GLU L1714 " pdb=" CA GLU L1714 " pdb=" CB GLU L1714 " ideal model delta sigma weight residual 110.49 140.03 -29.54 1.69e+00 3.50e-01 3.05e+02 angle pdb=" C ILE L1486 " pdb=" N PRO L1487 " pdb=" CA PRO L1487 " ideal model delta sigma weight residual 119.84 140.61 -20.77 1.25e+00 6.40e-01 2.76e+02 angle pdb=" N LEU L1713 " pdb=" CA LEU L1713 " pdb=" C LEU L1713 " ideal model delta sigma weight residual 110.80 76.13 34.67 2.13e+00 2.20e-01 2.65e+02 angle pdb=" CA PRO L1487 " pdb=" N PRO L1487 " pdb=" CD PRO L1487 " ideal model delta sigma weight residual 112.00 98.11 13.89 1.40e+00 5.10e-01 9.85e+01 ... (remaining 16113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6677 17.85 - 35.70: 460 35.70 - 53.54: 78 53.54 - 71.39: 16 71.39 - 89.24: 9 Dihedral angle restraints: 7240 sinusoidal: 3016 harmonic: 4224 Sorted by residual: dihedral pdb=" C LEU L1713 " pdb=" N LEU L1713 " pdb=" CA LEU L1713 " pdb=" CB LEU L1713 " ideal model delta harmonic sigma weight residual -122.60 -162.16 39.56 0 2.50e+00 1.60e-01 2.50e+02 dihedral pdb=" N GLU L1714 " pdb=" C GLU L1714 " pdb=" CA GLU L1714 " pdb=" CB GLU L1714 " ideal model delta harmonic sigma weight residual 122.80 153.98 -31.18 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" C GLU L1714 " pdb=" N GLU L1714 " pdb=" CA GLU L1714 " pdb=" CB GLU L1714 " ideal model delta harmonic sigma weight residual -122.60 -140.06 17.46 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.311: 1836 0.311 - 0.622: 0 0.622 - 0.934: 0 0.934 - 1.245: 1 1.245 - 1.556: 1 Chirality restraints: 1838 Sorted by residual: chirality pdb=" CA LEU L1713 " pdb=" N LEU L1713 " pdb=" C LEU L1713 " pdb=" CB LEU L1713 " both_signs ideal model delta sigma weight residual False 2.51 0.95 1.56 2.00e-01 2.50e+01 6.05e+01 chirality pdb=" CA GLU L1714 " pdb=" N GLU L1714 " pdb=" C GLU L1714 " pdb=" CB GLU L1714 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA ILE L1408 " pdb=" N ILE L1408 " pdb=" C ILE L1408 " pdb=" CB ILE L1408 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1835 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS L 450 " 0.063 5.00e-02 4.00e+02 9.37e-02 1.41e+01 pdb=" N PRO L 451 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO L 451 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO L 451 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L1666 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO L1667 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO L1667 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L1667 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G E 12 " -0.027 2.00e-02 2.50e+03 1.20e-02 4.28e+00 pdb=" N9 G E 12 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G E 12 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G E 12 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G E 12 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G E 12 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G E 12 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G E 12 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G E 12 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G E 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G E 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G E 12 " 0.001 2.00e-02 2.50e+03 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 118 2.63 - 3.20: 10364 3.20 - 3.76: 18448 3.76 - 4.33: 25693 4.33 - 4.90: 41967 Nonbonded interactions: 96590 Sorted by model distance: nonbonded pdb=" OD1 ASP L1332 " pdb="MG MG L2302 " model vdw 2.061 2.170 nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.073 3.040 nonbonded pdb="MG MG L2302 " pdb=" O HOH L2404 " model vdw 2.092 2.170 nonbonded pdb=" O ASN L1586 " pdb=" OG SER L1590 " model vdw 2.144 3.040 nonbonded pdb=" OG SER L1626 " pdb=" O2' U E 11 " model vdw 2.195 3.040 ... (remaining 96585 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: 2.030 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 0.230 11923 Z= 0.228 Angle : 0.772 51.090 16118 Z= 0.433 Chirality : 0.059 1.556 1838 Planarity : 0.004 0.094 2014 Dihedral : 12.848 89.240 4490 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.47 % Favored : 95.31 % Rotamer: Outliers : 0.08 % Allowed : 0.30 % Favored : 99.62 % Cbeta Deviations : 0.15 % 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: 0.83 (0.23), residues: 1411 helix: 1.60 (0.19), residues: 811 sheet: 1.10 (0.57), residues: 82 loop : -1.27 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L1347 TYR 0.034 0.001 TYR L1187 PHE 0.014 0.001 PHE L1277 TRP 0.018 0.001 TRP L 395 HIS 0.006 0.001 HIS L1298 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.23 (11920) covalent geometry : angle 0.77199 / 0.43 (16118) hydrogen bonds : bond 0.12313 / 8.71 ( 641) hydrogen bonds : angle 5.15943 / 3.83 ( 1845) metal coordination : bond 0.00154 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 40 MET cc_start: 0.7956 (tpp) cc_final: 0.7356 (tpp) REVERT: L 50 ILE cc_start: 0.8833 (mp) cc_final: 0.8597 (mm) REVERT: L 120 PHE cc_start: 0.8964 (t80) cc_final: 0.8633 (t80) REVERT: L 124 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8663 (mm-30) REVERT: L 137 LEU cc_start: 0.6459 (tp) cc_final: 0.5389 (mp) REVERT: L 188 GLU cc_start: 0.8711 (tt0) cc_final: 0.8463 (tp30) REVERT: L 1257 GLN cc_start: 0.7901 (pp30) cc_final: 0.7611 (pp30) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.7524 time to fit residues: 130.7529 Evaluate side-chains 89 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1407 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 19 ASN L 111 ASN L 287 HIS ** L 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1105 GLN L1184 HIS L1298 HIS L1481 GLN L1597 GLN L1798 HIS L1823 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.074525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050590 restraints weight = 56954.785| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.17 r_work: 0.2826 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11923 Z= 0.136 Angle : 0.605 9.036 16118 Z= 0.312 Chirality : 0.040 0.158 1838 Planarity : 0.005 0.065 2014 Dihedral : 5.497 61.756 1627 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.91 % Favored : 95.95 % Rotamer: Outliers : 0.99 % Allowed : 7.61 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.05 (0.23), residues: 1411 helix: 1.80 (0.18), residues: 823 sheet: 0.79 (0.55), residues: 82 loop : -1.20 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 716 TYR 0.023 0.001 TYR L1187 PHE 0.014 0.001 PHE L 783 TRP 0.014 0.001 TRP L 395 HIS 0.009 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11920) covalent geometry : angle 0.60516 / 0.31 (16118) hydrogen bonds : bond 0.04005 / 2.76 ( 641) hydrogen bonds : angle 4.18209 / 3.13 ( 1845) metal coordination : bond 0.00161 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7631 (p0) REVERT: L 40 MET cc_start: 0.7659 (tpp) cc_final: 0.7235 (tpp) REVERT: L 120 PHE cc_start: 0.9081 (t80) cc_final: 0.8815 (t80) REVERT: L 137 LEU cc_start: 0.7016 (tp) cc_final: 0.5800 (mp) REVERT: L 188 GLU cc_start: 0.8935 (tt0) cc_final: 0.8650 (tp30) REVERT: L 716 ARG cc_start: 0.8381 (mtp-110) cc_final: 0.8110 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8282 (pp30) cc_final: 0.7974 (pp30) REVERT: L 1509 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8887 (tm) REVERT: L 1599 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8092 (pt) outliers start: 13 outliers final: 4 residues processed: 104 average time/residue: 0.7093 time to fit residues: 79.0707 Evaluate side-chains 88 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1599 LEU Chi-restraints excluded: chain L residue 1780 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 140 optimal weight: 0.0770 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 379 ASN ** L 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1313 ASN L1798 HIS L1823 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.073913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050105 restraints weight = 61252.691| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.30 r_work: 0.2812 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11923 Z= 0.129 Angle : 0.560 9.334 16118 Z= 0.287 Chirality : 0.039 0.196 1838 Planarity : 0.004 0.062 2014 Dihedral : 5.402 61.773 1627 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 0.91 % Allowed : 7.84 % Favored : 91.25 % 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: 1.12 (0.23), residues: 1411 helix: 1.90 (0.18), residues: 822 sheet: 0.63 (0.56), residues: 82 loop : -1.22 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 716 TYR 0.021 0.001 TYR L1187 PHE 0.015 0.001 PHE L 783 TRP 0.011 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11920) covalent geometry : angle 0.55953 / 0.29 (16118) hydrogen bonds : bond 0.03784 / 2.60 ( 641) hydrogen bonds : angle 4.01330 / 3.00 ( 1845) metal coordination : bond 0.00143 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7241 (p0) REVERT: L 40 MET cc_start: 0.7700 (tpp) cc_final: 0.7298 (tpp) REVERT: L 137 LEU cc_start: 0.6917 (tp) cc_final: 0.5704 (mp) REVERT: L 188 GLU cc_start: 0.8964 (tt0) cc_final: 0.8688 (tp30) REVERT: L 716 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8129 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8374 (pp30) cc_final: 0.8025 (pp30) REVERT: L 1509 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8845 (tm) REVERT: L 1599 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8166 (pp) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 0.6569 time to fit residues: 68.0893 Evaluate side-chains 86 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1599 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 49 optimal weight: 0.0470 chunk 27 optimal weight: 0.0030 chunk 95 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 415 GLN L 720 GLN L1798 HIS L1823 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.074212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.050978 restraints weight = 53943.476| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.06 r_work: 0.2843 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11923 Z= 0.110 Angle : 0.544 11.297 16118 Z= 0.277 Chirality : 0.039 0.175 1838 Planarity : 0.004 0.059 2014 Dihedral : 5.295 61.900 1627 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.91 % Favored : 95.95 % Rotamer: Outliers : 0.91 % Allowed : 9.21 % Favored : 89.88 % 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: 1.24 (0.23), residues: 1411 helix: 1.99 (0.18), residues: 818 sheet: 0.42 (0.55), residues: 87 loop : -1.10 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 21 TYR 0.016 0.001 TYR L1187 PHE 0.012 0.001 PHE L 783 TRP 0.011 0.001 TRP L 395 HIS 0.012 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (11920) covalent geometry : angle 0.54445 / 0.28 (16118) hydrogen bonds : bond 0.03476 / 2.38 ( 641) hydrogen bonds : angle 3.90134 / 2.91 ( 1845) metal coordination : bond 0.00077 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 40 MET cc_start: 0.7688 (tpp) cc_final: 0.7282 (tpp) REVERT: L 137 LEU cc_start: 0.6887 (tp) cc_final: 0.5663 (mp) REVERT: L 188 GLU cc_start: 0.8935 (tt0) cc_final: 0.8657 (tp30) REVERT: L 716 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8137 (tpp-160) REVERT: L 1509 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8805 (tm) REVERT: L 1599 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8230 (pp) outliers start: 12 outliers final: 4 residues processed: 95 average time/residue: 0.6658 time to fit residues: 67.9410 Evaluate side-chains 81 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1599 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 19 ASN ** L1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1278 GLN L1798 HIS L1823 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.072679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049510 restraints weight = 41951.411| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.68 r_work: 0.2814 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11923 Z= 0.161 Angle : 0.559 7.972 16118 Z= 0.291 Chirality : 0.040 0.155 1838 Planarity : 0.004 0.055 2014 Dihedral : 5.326 61.139 1627 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 0.76 % Allowed : 10.05 % Favored : 89.19 % 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: 1.23 (0.23), residues: 1411 helix: 2.00 (0.18), residues: 818 sheet: 0.45 (0.55), residues: 87 loop : -1.15 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 343 TYR 0.019 0.001 TYR L1187 PHE 0.017 0.001 PHE L 120 TRP 0.009 0.001 TRP L 155 HIS 0.012 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11920) covalent geometry : angle 0.55944 / 0.29 (16118) hydrogen bonds : bond 0.03871 / 2.66 ( 641) hydrogen bonds : angle 3.95317 / 2.93 ( 1845) metal coordination : bond 0.00253 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 40 MET cc_start: 0.7710 (tpp) cc_final: 0.7292 (tpp) REVERT: L 137 LEU cc_start: 0.7003 (tp) cc_final: 0.5759 (mt) REVERT: L 188 GLU cc_start: 0.8872 (tt0) cc_final: 0.8628 (tp30) REVERT: L 446 MET cc_start: 0.9242 (tpp) cc_final: 0.9013 (tpt) REVERT: L 1509 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8955 (tm) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.6774 time to fit residues: 64.8200 Evaluate side-chains 80 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain L residue 489 LEU Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1509 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 18 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1798 HIS L1823 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.072559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049540 restraints weight = 41798.150| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.68 r_work: 0.2810 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11923 Z= 0.155 Angle : 0.573 9.192 16118 Z= 0.292 Chirality : 0.041 0.312 1838 Planarity : 0.004 0.055 2014 Dihedral : 5.303 60.820 1627 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.05 % Favored : 95.81 % Rotamer: Outliers : 0.68 % Allowed : 10.81 % Favored : 88.51 % 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: 1.20 (0.23), residues: 1411 helix: 1.94 (0.18), residues: 821 sheet: 0.45 (0.55), residues: 87 loop : -1.12 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 716 TYR 0.016 0.001 TYR L1187 PHE 0.015 0.001 PHE L 539 TRP 0.009 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (11920) covalent geometry : angle 0.57259 / 0.29 (16118) hydrogen bonds : bond 0.03813 / 2.61 ( 641) hydrogen bonds : angle 3.96553 / 2.94 ( 1845) metal coordination : bond 0.00227 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7087 (tp) cc_final: 0.5910 (mp) REVERT: L 141 ILE cc_start: 0.8291 (mm) cc_final: 0.8061 (mt) REVERT: L 188 GLU cc_start: 0.8992 (tt0) cc_final: 0.8703 (tp30) REVERT: L 446 MET cc_start: 0.9221 (tpp) cc_final: 0.8996 (tpt) REVERT: L 716 ARG cc_start: 0.8334 (mtp-110) cc_final: 0.8130 (tpp-160) REVERT: L 1675 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8185 (mp0) outliers start: 9 outliers final: 3 residues processed: 93 average time/residue: 0.6023 time to fit residues: 60.3258 Evaluate side-chains 84 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 489 LEU Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1675 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 59 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1597 GLN L1798 HIS L1823 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.073340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050203 restraints weight = 50580.285| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.95 r_work: 0.2824 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11923 Z= 0.115 Angle : 0.566 11.808 16118 Z= 0.283 Chirality : 0.040 0.304 1838 Planarity : 0.004 0.052 2014 Dihedral : 5.167 60.879 1627 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.05 % Favored : 95.81 % Rotamer: Outliers : 0.68 % Allowed : 10.96 % Favored : 88.36 % 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: 1411 helix: 2.00 (0.18), residues: 823 sheet: 0.47 (0.56), residues: 87 loop : -1.08 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 716 TYR 0.015 0.001 TYR L 183 PHE 0.016 0.001 PHE L 120 TRP 0.011 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11920) covalent geometry : angle 0.56597 / 0.28 (16118) hydrogen bonds : bond 0.03418 / 2.33 ( 641) hydrogen bonds : angle 3.85387 / 2.84 ( 1845) metal coordination : bond 0.00101 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7023 (tp) cc_final: 0.5803 (mt) REVERT: L 141 ILE cc_start: 0.8328 (mm) cc_final: 0.7869 (mt) REVERT: L 188 GLU cc_start: 0.8986 (tt0) cc_final: 0.8687 (tp30) REVERT: L 446 MET cc_start: 0.9249 (tpp) cc_final: 0.9016 (tpt) REVERT: L 716 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.8172 (tpp-160) REVERT: L 1598 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8071 (pptt) REVERT: L 1599 LEU cc_start: 0.8270 (pp) cc_final: 0.7958 (pp) REVERT: L 1675 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8219 (mp0) outliers start: 9 outliers final: 2 residues processed: 88 average time/residue: 0.6365 time to fit residues: 60.0311 Evaluate side-chains 80 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1675 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 7 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 68 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1798 HIS L1823 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.072775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048807 restraints weight = 70735.246| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.54 r_work: 0.2775 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11923 Z= 0.132 Angle : 0.552 9.823 16118 Z= 0.281 Chirality : 0.039 0.153 1838 Planarity : 0.004 0.051 2014 Dihedral : 5.016 60.629 1625 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.98 % Favored : 95.88 % Rotamer: Outliers : 0.68 % Allowed : 11.49 % Favored : 87.82 % 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: 1.30 (0.23), residues: 1411 helix: 2.04 (0.18), residues: 823 sheet: 0.49 (0.57), residues: 87 loop : -1.12 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 716 TYR 0.017 0.001 TYR L1226 PHE 0.014 0.001 PHE L 539 TRP 0.009 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11920) covalent geometry : angle 0.55194 / 0.28 (16118) hydrogen bonds : bond 0.03568 / 2.43 ( 641) hydrogen bonds : angle 3.88416 / 2.85 ( 1845) metal coordination : bond 0.00174 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7081 (tp) cc_final: 0.5854 (mt) REVERT: L 141 ILE cc_start: 0.8286 (mm) cc_final: 0.7810 (mt) REVERT: L 188 GLU cc_start: 0.8953 (tt0) cc_final: 0.8689 (tp30) REVERT: L 342 ARG cc_start: 0.7796 (mpt180) cc_final: 0.7592 (mpt180) REVERT: L 446 MET cc_start: 0.9268 (tpp) cc_final: 0.9035 (tpt) REVERT: L 716 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8229 (tpp-160) REVERT: L 1407 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8746 (t0) REVERT: L 1675 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8257 (mp0) outliers start: 9 outliers final: 3 residues processed: 87 average time/residue: 0.6228 time to fit residues: 58.4237 Evaluate side-chains 84 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1675 GLU Chi-restraints excluded: chain L residue 1823 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1278 GLN L1798 HIS L1823 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.072900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049319 restraints weight = 57879.109| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.18 r_work: 0.2795 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11923 Z= 0.128 Angle : 0.584 13.464 16118 Z= 0.289 Chirality : 0.040 0.376 1838 Planarity : 0.004 0.050 2014 Dihedral : 4.990 60.484 1625 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 0.61 % Allowed : 11.49 % Favored : 87.90 % 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: 1411 helix: 1.98 (0.18), residues: 825 sheet: 0.31 (0.56), residues: 89 loop : -1.06 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 716 TYR 0.017 0.001 TYR L1226 PHE 0.014 0.001 PHE L 120 TRP 0.009 0.001 TRP L 395 HIS 0.013 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11920) covalent geometry : angle 0.58356 / 0.29 (16118) hydrogen bonds : bond 0.03501 / 2.40 ( 641) hydrogen bonds : angle 3.89715 / 2.85 ( 1845) metal coordination : bond 0.00152 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7069 (tp) cc_final: 0.5865 (mt) REVERT: L 141 ILE cc_start: 0.8354 (mm) cc_final: 0.7908 (mt) REVERT: L 188 GLU cc_start: 0.8992 (tt0) cc_final: 0.8725 (tp30) REVERT: L 446 MET cc_start: 0.9251 (tpp) cc_final: 0.9015 (tpt) REVERT: L 716 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.8208 (tpp-160) REVERT: L 1407 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8724 (t0) REVERT: L 1598 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8063 (pptt) REVERT: L 1599 LEU cc_start: 0.8381 (pp) cc_final: 0.8081 (pt) REVERT: L 1675 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8268 (mp0) outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.6453 time to fit residues: 59.8789 Evaluate side-chains 84 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1675 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 88 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1798 HIS L1823 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.073341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049933 restraints weight = 60653.790| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.26 r_work: 0.2814 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11923 Z= 0.106 Angle : 0.567 13.227 16118 Z= 0.281 Chirality : 0.039 0.225 1838 Planarity : 0.003 0.050 2014 Dihedral : 4.928 60.541 1625 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 0.61 % Allowed : 11.42 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1411 helix: 2.02 (0.18), residues: 827 sheet: 0.51 (0.57), residues: 87 loop : -1.05 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 716 TYR 0.015 0.001 TYR L 183 PHE 0.013 0.001 PHE L 539 TRP 0.010 0.001 TRP L 395 HIS 0.007 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (11920) covalent geometry : angle 0.56713 / 0.28 (16118) hydrogen bonds : bond 0.03320 / 2.27 ( 641) hydrogen bonds : angle 3.81792 / 2.79 ( 1845) metal coordination : bond 0.00077 / 0.04 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7098 (tp) cc_final: 0.5895 (mt) REVERT: L 141 ILE cc_start: 0.8196 (mm) cc_final: 0.7963 (mt) REVERT: L 188 GLU cc_start: 0.8946 (tt0) cc_final: 0.8708 (tp30) REVERT: L 342 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7217 (mmp80) REVERT: L 716 ARG cc_start: 0.8480 (mtp-110) cc_final: 0.8235 (tpp-160) REVERT: L 1407 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8734 (t0) REVERT: L 1598 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8023 (pptt) REVERT: L 1599 LEU cc_start: 0.8209 (pp) cc_final: 0.7865 (pt) REVERT: L 1675 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8242 (mp0) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 0.6514 time to fit residues: 62.7383 Evaluate side-chains 86 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Chi-restraints excluded: chain L residue 1675 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 138 optimal weight: 4.9990 chunk 56 optimal weight: 0.0570 chunk 134 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 0.0570 chunk 64 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1798 HIS L1823 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.073134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049129 restraints weight = 88586.665| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.94 r_work: 0.2771 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11923 Z= 0.117 Angle : 0.592 13.001 16118 Z= 0.289 Chirality : 0.040 0.385 1838 Planarity : 0.004 0.049 2014 Dihedral : 4.902 60.430 1625 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 0.61 % Allowed : 11.57 % Favored : 87.82 % 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: 1.33 (0.23), residues: 1411 helix: 2.03 (0.18), residues: 825 sheet: 0.55 (0.57), residues: 87 loop : -1.07 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 716 TYR 0.028 0.001 TYR L 116 PHE 0.015 0.001 PHE L 120 TRP 0.009 0.001 TRP L 395 HIS 0.008 0.001 HIS L1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11920) covalent geometry : angle 0.59237 / 0.29 (16118) hydrogen bonds : bond 0.03392 / 2.31 ( 641) hydrogen bonds : angle 3.84576 / 2.79 ( 1845) metal coordination : bond 0.00117 / 0.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4246.43 seconds wall clock time: 73 minutes 5.37 seconds (4385.37 seconds total)