Starting phenix.real_space_refine on Wed Jul 30 05:39:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oea_12862/07_2025/7oea_12862.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oea_12862/07_2025/7oea_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2025/7oea_12862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2025/7oea_12862.map" model { file = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2025/7oea_12862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oea_12862/07_2025/7oea_12862.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.82, per 1000 atoms: 1.01 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: 2.61 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 1.37 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: 4.69 Time building geometry restraints manager: 3.15 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: 6689 17.85 - 35.70: 461 35.70 - 53.54: 88 53.54 - 71.39: 25 71.39 - 89.24: 11 Dihedral angle restraints: 7274 sinusoidal: 3050 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 7271 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: 1.390 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 37.750 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 13.353 89.240 4524 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (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 TRP 0.018 0.001 TRP L 395 HIS 0.006 0.001 HIS L1298 PHE 0.014 0.001 PHE L1277 TYR 0.034 0.001 TYR L1187 ARG 0.004 0.000 ARG L1347 Details of bonding type rmsd hydrogen bonds : bond 0.12313 ( 641) hydrogen bonds : angle 5.15943 ( 1845) metal coordination : bond 0.00154 ( 3) covalent geometry : bond 0.00372 (11920) covalent geometry : angle 0.77199 (16118) *********************** 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 : 1.269 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: 1.7087 time to fit residues: 297.8611 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 : 1.231 ------------------------------------------------------------------------------- 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 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3638 r_free = 0.3638 target = 0.074217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.050249 restraints weight = 56674.430| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.16 r_work: 0.2817 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 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 = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1890 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= 0.141 Angle : 0.607 9.097 16118 Z= 0.313 Chirality : 0.040 0.157 1838 Planarity : 0.005 0.066 2014 Dihedral : 8.172 73.454 1661 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1411 helix: 1.79 (0.18), residues: 823 sheet: 0.90 (0.56), residues: 80 loop : -1.20 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 395 HIS 0.009 0.001 HIS L1823 PHE 0.015 0.001 PHE L 783 TYR 0.024 0.001 TYR L1187 ARG 0.011 0.001 ARG L 343 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 641) hydrogen bonds : angle 4.18390 ( 1845) metal coordination : bond 0.00193 ( 3) covalent geometry : bond 0.00330 (11920) covalent geometry : angle 0.60696 (16118) *********************** 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 109 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7522 (p0) REVERT: L 40 MET cc_start: 0.7651 (tpp) cc_final: 0.7235 (tpp) REVERT: L 120 PHE cc_start: 0.9073 (t80) cc_final: 0.8812 (t80) REVERT: L 137 LEU cc_start: 0.7040 (tp) cc_final: 0.5829 (mp) REVERT: L 188 GLU cc_start: 0.8959 (tt0) cc_final: 0.8671 (tp30) REVERT: L 716 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.8112 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8289 (pp30) cc_final: 0.7986 (pp30) REVERT: L 1509 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8892 (tm) REVERT: L 1599 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8087 (pt) outliers start: 13 outliers final: 4 residues processed: 105 average time/residue: 1.5390 time to fit residues: 173.7945 Evaluate side-chains 86 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 92 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 379 ASN ** L 415 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.072627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048992 restraints weight = 50400.771| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.96 r_work: 0.2791 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2162 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= 0.184 Angle : 0.595 9.299 16118 Z= 0.306 Chirality : 0.041 0.203 1838 Planarity : 0.004 0.062 2014 Dihedral : 8.173 73.367 1661 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.33 % Favored : 95.53 % Rotamer: Outliers : 0.99 % Allowed : 7.91 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1411 helix: 1.79 (0.18), residues: 824 sheet: 0.60 (0.54), residues: 87 loop : -1.17 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 PHE 0.018 0.001 PHE L 783 TYR 0.024 0.001 TYR L1187 ARG 0.008 0.001 ARG L 716 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 641) hydrogen bonds : angle 4.11166 ( 1845) metal coordination : bond 0.00304 ( 3) covalent geometry : bond 0.00425 (11920) covalent geometry : angle 0.59451 (16118) *********************** 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 101 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 40 MET cc_start: 0.7718 (tpp) cc_final: 0.7261 (tpp) REVERT: L 137 LEU cc_start: 0.6984 (tp) cc_final: 0.5772 (mp) REVERT: L 188 GLU cc_start: 0.8960 (tt0) cc_final: 0.8709 (tp30) REVERT: L 716 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.8129 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8386 (pp30) cc_final: 0.8033 (pp30) REVERT: L 1509 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8948 (tm) REVERT: L 1599 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8213 (pp) outliers start: 13 outliers final: 3 residues processed: 97 average time/residue: 1.4192 time to fit residues: 149.1201 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 : 1.243 ------------------------------------------------------------------------------- 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 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 89 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 13 optimal weight: 0.0970 chunk 97 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 720 GLN 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 = 0.3633 r_free = 0.3633 target = 0.073695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050890 restraints weight = 40159.973| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.62 r_work: 0.2852 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11923 Z= 0.112 Angle : 0.543 8.561 16118 Z= 0.277 Chirality : 0.039 0.190 1838 Planarity : 0.004 0.058 2014 Dihedral : 8.064 73.448 1661 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.05 % Favored : 95.81 % Rotamer: Outliers : 0.68 % Allowed : 9.28 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1411 helix: 1.95 (0.18), residues: 820 sheet: 0.45 (0.55), residues: 87 loop : -1.16 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 PHE 0.019 0.001 PHE L 120 TYR 0.016 0.001 TYR L1187 ARG 0.008 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 641) hydrogen bonds : angle 3.91059 ( 1845) metal coordination : bond 0.00069 ( 3) covalent geometry : bond 0.00257 (11920) covalent geometry : angle 0.54282 (16118) *********************** 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 95 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 40 MET cc_start: 0.7738 (tpp) cc_final: 0.7332 (tpp) REVERT: L 137 LEU cc_start: 0.6957 (tp) cc_final: 0.5715 (mt) REVERT: L 188 GLU cc_start: 0.8935 (tt0) cc_final: 0.8666 (tp30) REVERT: L 716 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8096 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8419 (pp30) cc_final: 0.8069 (pp30) REVERT: L 1509 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8871 (tm) REVERT: L 1689 MET cc_start: 0.8560 (tmm) cc_final: 0.8277 (tmm) outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 1.9116 time to fit residues: 192.2136 Evaluate side-chains 82 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 415 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 = 0.3607 r_free = 0.3607 target = 0.072525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048443 restraints weight = 70190.280| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.53 r_work: 0.2760 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 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 = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11923 Z= 0.157 Angle : 0.555 7.923 16118 Z= 0.288 Chirality : 0.040 0.156 1838 Planarity : 0.004 0.055 2014 Dihedral : 8.058 73.471 1661 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.33 % Favored : 95.53 % Rotamer: Outliers : 0.84 % Allowed : 9.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.23), residues: 1411 helix: 1.96 (0.18), residues: 822 sheet: 0.44 (0.55), residues: 87 loop : -1.16 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 PHE 0.015 0.001 PHE L 783 TYR 0.018 0.001 TYR L1187 ARG 0.005 0.000 ARG L 716 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 641) hydrogen bonds : angle 3.93600 ( 1845) metal coordination : bond 0.00232 ( 3) covalent geometry : bond 0.00363 (11920) covalent geometry : angle 0.55531 (16118) *********************** 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 95 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7122 (tp) cc_final: 0.5888 (mt) REVERT: L 188 GLU cc_start: 0.9022 (tt0) cc_final: 0.8733 (tp30) REVERT: L 574 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8246 (t80) REVERT: L 1257 GLN cc_start: 0.8501 (pp30) cc_final: 0.8153 (pp30) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 1.4858 time to fit residues: 146.0335 Evaluate side-chains 88 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 574 TYR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 3 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 56 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.0050 overall best weight: 0.2630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 415 GLN ** L 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3637 r_free = 0.3637 target = 0.073835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050098 restraints weight = 70336.350| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.53 r_work: 0.2807 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 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 = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11923 Z= 0.104 Angle : 0.535 9.747 16118 Z= 0.274 Chirality : 0.038 0.186 1838 Planarity : 0.004 0.054 2014 Dihedral : 8.009 73.436 1661 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 0.84 % Allowed : 10.58 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1411 helix: 2.03 (0.18), residues: 822 sheet: 0.45 (0.55), residues: 87 loop : -1.11 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 PHE 0.016 0.001 PHE L 120 TYR 0.016 0.001 TYR L 116 ARG 0.013 0.000 ARG L 716 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 641) hydrogen bonds : angle 3.81414 ( 1845) metal coordination : bond 0.00019 ( 3) covalent geometry : bond 0.00237 (11920) covalent geometry : angle 0.53511 (16118) *********************** 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 101 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7063 (tp) cc_final: 0.5831 (mt) REVERT: L 188 GLU cc_start: 0.8990 (tt0) cc_final: 0.8705 (tp30) REVERT: L 574 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.8230 (t80) REVERT: L 716 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.8150 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8513 (pp30) cc_final: 0.8147 (pp30) REVERT: L 1675 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: L 1689 MET cc_start: 0.8664 (tmm) cc_final: 0.8383 (tmm) outliers start: 11 outliers final: 3 residues processed: 98 average time/residue: 1.5029 time to fit residues: 158.9544 Evaluate side-chains 83 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 574 TYR Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1509 LEU 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 86 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.0010 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3631 r_free = 0.3631 target = 0.073561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051068 restraints weight = 36505.460| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.50 r_work: 0.2863 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2700 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= 0.111 Angle : 0.563 9.476 16118 Z= 0.284 Chirality : 0.040 0.368 1838 Planarity : 0.004 0.054 2014 Dihedral : 7.849 73.423 1659 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.76 % Favored : 96.09 % Rotamer: Outliers : 0.91 % Allowed : 10.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1411 helix: 2.08 (0.18), residues: 823 sheet: 0.54 (0.56), residues: 87 loop : -1.08 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 395 HIS 0.012 0.001 HIS L1823 PHE 0.015 0.001 PHE L 539 TYR 0.028 0.001 TYR L 183 ARG 0.011 0.001 ARG L 716 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 641) hydrogen bonds : angle 3.82537 ( 1845) metal coordination : bond 0.00093 ( 3) covalent geometry : bond 0.00256 (11920) covalent geometry : angle 0.56330 (16118) *********************** 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 98 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7068 (tp) cc_final: 0.5855 (mt) REVERT: L 188 GLU cc_start: 0.8981 (tt0) cc_final: 0.8703 (tp30) REVERT: L 574 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8368 (t80) REVERT: L 716 ARG cc_start: 0.8535 (mtp-110) cc_final: 0.8285 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8515 (pp30) cc_final: 0.8155 (pp30) REVERT: L 1407 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8777 (t0) REVERT: L 1598 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8075 (pptt) REVERT: L 1599 LEU cc_start: 0.8286 (pp) cc_final: 0.7962 (pp) REVERT: L 1675 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: L 1689 MET cc_start: 0.8783 (tmm) cc_final: 0.8509 (tmm) outliers start: 12 outliers final: 4 residues processed: 94 average time/residue: 1.5123 time to fit residues: 153.5284 Evaluate side-chains 85 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 574 TYR 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 1675 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 142 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3626 r_free = 0.3626 target = 0.073293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049875 restraints weight = 61286.731| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.28 r_work: 0.2810 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2762 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 : 0.565 11.031 16118 Z= 0.286 Chirality : 0.040 0.363 1838 Planarity : 0.004 0.051 2014 Dihedral : 7.850 73.429 1659 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 0.61 % Allowed : 11.80 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1411 helix: 2.04 (0.18), residues: 822 sheet: 0.51 (0.56), residues: 87 loop : -1.08 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 395 HIS 0.011 0.001 HIS L1823 PHE 0.014 0.001 PHE L 120 TYR 0.025 0.001 TYR L 183 ARG 0.016 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 641) hydrogen bonds : angle 3.84968 ( 1845) metal coordination : bond 0.00118 ( 3) covalent geometry : bond 0.00269 (11920) covalent geometry : angle 0.56518 (16118) *********************** 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: 8 poor density : 81 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7098 (tp) cc_final: 0.5864 (mt) REVERT: L 188 GLU cc_start: 0.8989 (tt0) cc_final: 0.8704 (tp30) REVERT: L 574 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8224 (t80) REVERT: L 716 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.8210 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8486 (pp30) cc_final: 0.8124 (pp30) REVERT: L 1407 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8717 (t0) REVERT: L 1598 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8029 (pptt) REVERT: L 1599 LEU cc_start: 0.8279 (pp) cc_final: 0.7974 (pp) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 1.7955 time to fit residues: 168.3079 Evaluate side-chains 86 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 574 TYR 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 1823 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1823 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.073120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049922 restraints weight = 50171.174| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.96 r_work: 0.2814 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2802 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= 0.126 Angle : 0.567 11.650 16118 Z= 0.287 Chirality : 0.039 0.201 1838 Planarity : 0.004 0.050 2014 Dihedral : 7.847 73.435 1659 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.91 % Favored : 95.95 % Rotamer: Outliers : 0.53 % Allowed : 11.72 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.23), residues: 1411 helix: 2.07 (0.18), residues: 820 sheet: 0.51 (0.57), residues: 87 loop : -1.08 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.019 0.001 HIS L1823 PHE 0.014 0.001 PHE L 539 TYR 0.023 0.001 TYR L 183 ARG 0.016 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 641) hydrogen bonds : angle 3.85083 ( 1845) metal coordination : bond 0.00152 ( 3) covalent geometry : bond 0.00291 (11920) covalent geometry : angle 0.56719 (16118) *********************** 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 89 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7108 (tp) cc_final: 0.5874 (mt) REVERT: L 184 SER cc_start: 0.9456 (t) cc_final: 0.9174 (p) REVERT: L 188 GLU cc_start: 0.9015 (tt0) cc_final: 0.8741 (tp30) REVERT: L 574 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8211 (t80) REVERT: L 716 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.8210 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8515 (pp30) cc_final: 0.8150 (pp30) REVERT: L 1407 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8727 (t0) REVERT: L 1598 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8020 (pptt) REVERT: L 1599 LEU cc_start: 0.8272 (pp) cc_final: 0.7993 (pp) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 1.5410 time to fit residues: 144.7701 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 : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 574 TYR 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 1823 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1823 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.073207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049465 restraints weight = 67436.687| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.46 r_work: 0.2792 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2861 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= 0.120 Angle : 0.596 12.789 16118 Z= 0.295 Chirality : 0.040 0.384 1838 Planarity : 0.004 0.050 2014 Dihedral : 7.850 73.430 1659 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.12 % Favored : 95.81 % Rotamer: Outliers : 0.38 % Allowed : 12.10 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1411 helix: 2.01 (0.18), residues: 824 sheet: 0.52 (0.56), residues: 87 loop : -1.04 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 395 HIS 0.016 0.001 HIS L1823 PHE 0.015 0.001 PHE L 120 TYR 0.023 0.001 TYR L 183 ARG 0.020 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 641) hydrogen bonds : angle 3.86773 ( 1845) metal coordination : bond 0.00122 ( 3) covalent geometry : bond 0.00278 (11920) covalent geometry : angle 0.59551 (16118) ********************** 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 84 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 137 LEU cc_start: 0.7155 (tp) cc_final: 0.5920 (mt) REVERT: L 184 SER cc_start: 0.9461 (t) cc_final: 0.9176 (p) REVERT: L 188 GLU cc_start: 0.9054 (tt0) cc_final: 0.8787 (tp30) REVERT: L 574 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8256 (t80) REVERT: L 716 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.8242 (tpp-160) REVERT: L 1257 GLN cc_start: 0.8554 (pp30) cc_final: 0.8203 (pp30) REVERT: L 1407 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8725 (t0) REVERT: L 1598 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8096 (pptt) outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 1.5235 time to fit residues: 135.0734 Evaluate side-chains 83 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 574 TYR Chi-restraints excluded: chain L residue 1298 HIS Chi-restraints excluded: chain L residue 1346 GLN Chi-restraints excluded: chain L residue 1407 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 111 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1798 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.073033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049472 restraints weight = 62586.578| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.31 r_work: 0.2795 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2898 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= 0.124 Angle : 0.591 12.569 16118 Z= 0.293 Chirality : 0.041 0.386 1838 Planarity : 0.004 0.050 2014 Dihedral : 7.844 73.429 1659 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.12 % Favored : 95.81 % Rotamer: Outliers : 0.38 % Allowed : 11.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1411 helix: 2.03 (0.18), residues: 821 sheet: 0.75 (0.59), residues: 80 loop : -1.10 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 395 HIS 0.003 0.001 HIS L 736 PHE 0.014 0.001 PHE L 539 TYR 0.023 0.001 TYR L 183 ARG 0.020 0.001 ARG L 21 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 641) hydrogen bonds : angle 3.88594 ( 1845) metal coordination : bond 0.00155 ( 3) covalent geometry : bond 0.00288 (11920) covalent geometry : angle 0.59124 (16118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10944.81 seconds wall clock time: 195 minutes 1.63 seconds (11701.63 seconds total)