Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 06:22:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oeb_12863/04_2023/7oeb_12863.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oeb_12863/04_2023/7oeb_12863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oeb_12863/04_2023/7oeb_12863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oeb_12863/04_2023/7oeb_12863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oeb_12863/04_2023/7oeb_12863.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oeb_12863/04_2023/7oeb_12863.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 7425 2.51 5 N 1967 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 102": "OE1" <-> "OE2" Residue "L GLU 179": "OE1" <-> "OE2" Residue "L GLU 188": "OE1" <-> "OE2" Residue "L GLU 608": "OE1" <-> "OE2" Residue "L GLU 663": "OE1" <-> "OE2" Residue "L GLU 686": "OE1" <-> "OE2" Residue "L GLU 725": "OE1" <-> "OE2" Residue "L GLU 1343": "OE1" <-> "OE2" Residue "L GLU 1698": "OE1" <-> "OE2" Residue "L GLU 1706": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11682 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 11549 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1434, 11539 Classifications: {'peptide': 1434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1387} Chain breaks: 11 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1434, 11539 Classifications: {'peptide': 1434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1387} Chain breaks: 11 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 11745 Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2483 SG CYS L 321 38.338 100.395 64.570 1.00 54.49 S ATOM 2860 SG CYS L 366 38.027 99.920 68.094 1.00 69.97 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS L1435 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS L1435 " occ=0.50 Time building chain proxies: 11.90, per 1000 atoms: 1.02 Number of scatterers: 11682 At special positions: 0 Unit cell: (118.261, 131.493, 101.721, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 6 15.00 Mg 2 11.99 O 2208 8.00 N 1967 7.00 C 7425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.72 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 321 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 59.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 19 through 32 removed outlier: 4.550A pdb=" N ARG L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 58 Processing helix chain 'L' and resid 68 through 76 Processing helix chain 'L' and resid 108 through 131 Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 153 through 175 Processing helix chain 'L' and resid 179 through 191 Processing helix chain 'L' and resid 199 through 204 Processing helix chain 'L' and resid 211 through 223 removed outlier: 3.731A pdb=" N GLU L 215 " --> pdb=" O SER L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 251 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 273 through 275 No H-bonds generated for 'chain 'L' and resid 273 through 275' Processing helix chain 'L' and resid 284 through 293 Processing helix chain 'L' and resid 296 through 303 Processing helix chain 'L' and resid 321 through 336 removed outlier: 3.533A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 365 Processing helix chain 'L' and resid 385 through 404 Processing helix chain 'L' and resid 412 through 435 removed outlier: 3.527A pdb=" N ASP L 434 " --> pdb=" O ALA L 430 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL L 435 " --> pdb=" O ALA L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 442 Processing helix chain 'L' and resid 445 through 449 removed outlier: 3.614A pdb=" N VAL L 448 " --> pdb=" O ASN L 445 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 459 Processing helix chain 'L' and resid 491 through 507 Processing helix chain 'L' and resid 508 through 510 No H-bonds generated for 'chain 'L' and resid 508 through 510' Processing helix chain 'L' and resid 576 through 580 removed outlier: 3.538A pdb=" N TYR L 580 " --> pdb=" O PRO L 577 " (cutoff:3.500A) Processing helix chain 'L' and resid 586 through 601 removed outlier: 3.910A pdb=" N VAL L 601 " --> pdb=" O MET L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 608 Processing helix chain 'L' and resid 610 through 628 removed outlier: 3.917A pdb=" N ILE L 614 " --> pdb=" O GLN L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 648 removed outlier: 3.709A pdb=" N LEU L 640 " --> pdb=" O LEU L 636 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 655 through 661 removed outlier: 3.570A pdb=" N ARG L 661 " --> pdb=" O ILE L 657 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 684 Processing helix chain 'L' and resid 691 through 705 Processing helix chain 'L' and resid 706 through 708 No H-bonds generated for 'chain 'L' and resid 706 through 708' Processing helix chain 'L' and resid 715 through 735 Proline residue: L 730 - end of helix Processing helix chain 'L' and resid 746 through 761 removed outlier: 3.667A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 1089 through 1096 Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 3.741A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1165 through 1182 removed outlier: 3.741A pdb=" N PHE L1169 " --> pdb=" O ASN L1165 " (cutoff:3.500A) Processing helix chain 'L' and resid 1193 through 1198 Processing helix chain 'L' and resid 1199 through 1210 Processing helix chain 'L' and resid 1219 through 1236 Processing helix chain 'L' and resid 1242 through 1259 Processing helix chain 'L' and resid 1267 through 1278 Processing helix chain 'L' and resid 1297 through 1320 Processing helix chain 'L' and resid 1338 through 1348 Processing helix chain 'L' and resid 1348 through 1366 Processing helix chain 'L' and resid 1396 through 1407 Processing helix chain 'L' and resid 1412 through 1431 Processing helix chain 'L' and resid 1433 through 1451 Processing helix chain 'L' and resid 1465 through 1471 removed outlier: 3.729A pdb=" N TRP L1469 " --> pdb=" O ASP L1465 " (cutoff:3.500A) Processing helix chain 'L' and resid 1473 through 1486 Processing helix chain 'L' and resid 1486 through 1507 removed outlier: 3.631A pdb=" N CYS L1490 " --> pdb=" O ILE L1486 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY L1491 " --> pdb=" O PRO L1487 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG L1492 " --> pdb=" O ASP L1488 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE L1493 " --> pdb=" O ALA L1489 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY L1507 " --> pdb=" O LYS L1503 " (cutoff:3.500A) Processing helix chain 'L' and resid 1524 through 1533 removed outlier: 4.025A pdb=" N ASN L1528 " --> pdb=" O SER L1524 " (cutoff:3.500A) Processing helix chain 'L' and resid 1541 through 1543 No H-bonds generated for 'chain 'L' and resid 1541 through 1543' Processing helix chain 'L' and resid 1579 through 1589 Processing helix chain 'L' and resid 1595 through 1608 removed outlier: 4.101A pdb=" N ALA L1608 " --> pdb=" O ILE L1604 " (cutoff:3.500A) Processing helix chain 'L' and resid 1612 through 1626 Processing helix chain 'L' and resid 1638 through 1649 removed outlier: 3.791A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1674 through 1679 removed outlier: 4.408A pdb=" N ILE L1678 " --> pdb=" O ASN L1674 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER L1679 " --> pdb=" O GLU L1675 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1674 through 1679' Processing helix chain 'L' and resid 1684 through 1700 Processing helix chain 'L' and resid 1701 through 1705 Processing helix chain 'L' and resid 1778 through 1790 removed outlier: 4.045A pdb=" N LEU L1782 " --> pdb=" O LYS L1778 " (cutoff:3.500A) Processing helix chain 'L' and resid 1795 through 1800 removed outlier: 3.754A pdb=" N HIS L1798 " --> pdb=" O LEU L1795 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE L1799 " --> pdb=" O VAL L1796 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL L1800 " --> pdb=" O SER L1797 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1795 through 1800' Processing helix chain 'L' and resid 1812 through 1817 Processing sheet with id=AA1, first strand: chain 'L' and resid 61 through 62 removed outlier: 6.465A pdb=" N LEU L 98 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'L' and resid 207 through 208 removed outlier: 6.367A pdb=" N LEU L 207 " --> pdb=" O TYR L1107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 258 through 260 Processing sheet with id=AA5, first strand: chain 'L' and resid 374 through 377 removed outlier: 3.726A pdb=" N ARG L 381 " --> pdb=" O SER L 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 738 through 739 removed outlier: 7.073A pdb=" N PHE L1119 " --> pdb=" O GLU L1240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1381 through 1383 Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 8.925A pdb=" N GLN L1662 " --> pdb=" O LEU L1548 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU L1548 " --> pdb=" O GLN L1662 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 1629 through 1630 Processing sheet with id=AB1, first strand: chain 'L' and resid 1723 through 1726 645 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3356 1.33 - 1.45: 1834 1.45 - 1.57: 6604 1.57 - 1.69: 11 1.69 - 1.81: 107 Bond restraints: 11912 Sorted by residual: bond pdb=" N ILE L 348 " pdb=" CA ILE L 348 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.10e+00 bond pdb=" N VAL L1712 " pdb=" CA VAL L1712 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.76e+00 bond pdb=" N GLN L1333 " pdb=" CA GLN L1333 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.60e+00 bond pdb=" N ASP L1332 " pdb=" CA ASP L1332 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.84e+00 bond pdb=" N ASP L 350 " pdb=" CA ASP L 350 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.24e+00 ... (remaining 11907 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.77: 212 105.77 - 112.83: 6475 112.83 - 119.88: 3934 119.88 - 126.93: 5357 126.93 - 133.99: 124 Bond angle restraints: 16102 Sorted by residual: angle pdb=" N LYS L 602 " pdb=" CA LYS L 602 " pdb=" C LYS L 602 " ideal model delta sigma weight residual 114.62 110.76 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA ASP L1332 " pdb=" C ASP L1332 " pdb=" O ASP L1332 " ideal model delta sigma weight residual 121.56 117.92 3.64 1.09e+00 8.42e-01 1.12e+01 angle pdb=" N ASP L1331 " pdb=" CA ASP L1331 " pdb=" C ASP L1331 " ideal model delta sigma weight residual 114.04 109.94 4.10 1.24e+00 6.50e-01 1.09e+01 angle pdb=" O ILE L 348 " pdb=" C ILE L 348 " pdb=" N PHE L 349 " ideal model delta sigma weight residual 121.91 124.65 -2.74 9.80e-01 1.04e+00 7.80e+00 angle pdb=" CA ILE L 348 " pdb=" C ILE L 348 " pdb=" O ILE L 348 " ideal model delta sigma weight residual 121.17 118.23 2.94 1.06e+00 8.90e-01 7.68e+00 ... (remaining 16097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.21: 6565 18.21 - 36.43: 535 36.43 - 54.64: 98 54.64 - 72.85: 24 72.85 - 91.07: 16 Dihedral angle restraints: 7238 sinusoidal: 3008 harmonic: 4230 Sorted by residual: dihedral pdb=" CA ILE L1670 " pdb=" C ILE L1670 " pdb=" N ARG L1671 " pdb=" CA ARG L1671 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA VAL L 275 " pdb=" C VAL L 275 " pdb=" N ASP L 276 " pdb=" CA ASP L 276 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA MET L1198 " pdb=" C MET L1198 " pdb=" N CYS L1199 " pdb=" CA CYS L1199 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 7235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1217 0.036 - 0.071: 452 0.071 - 0.107: 123 0.107 - 0.143: 34 0.143 - 0.179: 9 Chirality restraints: 1835 Sorted by residual: chirality pdb=" CB ILE L 138 " pdb=" CA ILE L 138 " pdb=" CG1 ILE L 138 " pdb=" CG2 ILE L 138 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA VAL L1712 " pdb=" N VAL L1712 " pdb=" C VAL L1712 " pdb=" CB VAL L1712 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA ILE L1376 " pdb=" N ILE L1376 " pdb=" C ILE L1376 " pdb=" CB ILE L1376 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 1832 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L1666 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO L1667 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO L1667 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO L1667 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L1486 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO L1487 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO L1487 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L1487 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G E 12 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.06e+00 pdb=" N9 G E 12 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G E 12 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G E 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G E 12 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G E 12 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G E 12 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G E 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G E 12 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G E 12 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G E 12 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G E 12 " 0.003 2.00e-02 2.50e+03 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 181 2.68 - 3.23: 11139 3.23 - 3.79: 18525 3.79 - 4.34: 25058 4.34 - 4.90: 41163 Nonbonded interactions: 96066 Sorted by model distance: nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.121 2.440 nonbonded pdb=" O ASN L1586 " pdb=" OG SER L1590 " model vdw 2.164 2.440 nonbonded pdb=" NH2 ARG L1452 " pdb=" OP1 U E 13 " model vdw 2.181 2.520 nonbonded pdb=" OD2 ASP L1332 " pdb=" N LYS L1384 " model vdw 2.212 2.520 nonbonded pdb=" OG SER L1626 " pdb=" O2' U E 11 " model vdw 2.225 2.440 ... (remaining 96061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.910 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: 7.850 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 43.210 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11912 Z= 0.227 Angle : 0.557 6.880 16102 Z= 0.313 Chirality : 0.042 0.179 1835 Planarity : 0.004 0.077 2015 Dihedral : 14.394 91.066 4484 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.74 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1413 helix: 1.77 (0.18), residues: 797 sheet: -0.13 (0.51), residues: 101 loop : -1.06 (0.27), residues: 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 172 average time/residue: 0.3429 time to fit residues: 77.7979 Evaluate side-chains 89 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1125 time to fit residues: 2.1681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN L 175 ASN L 359 HIS L 720 GLN L1105 GLN L1346 GLN L1481 GLN L1516 ASN L1554 HIS L1798 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11912 Z= 0.184 Angle : 0.532 9.262 16102 Z= 0.271 Chirality : 0.039 0.145 1835 Planarity : 0.004 0.064 2015 Dihedral : 4.969 68.275 1615 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer Outliers : 0.76 % 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: 1413 helix: 2.08 (0.18), residues: 806 sheet: 0.29 (0.55), residues: 89 loop : -1.00 (0.27), residues: 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 0.3024 time to fit residues: 40.7039 Evaluate side-chains 83 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1102 time to fit residues: 3.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 140 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11912 Z= 0.207 Angle : 0.514 8.937 16102 Z= 0.262 Chirality : 0.039 0.156 1835 Planarity : 0.004 0.057 2015 Dihedral : 4.925 67.553 1615 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer Outliers : 0.23 % 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: 1.40 (0.23), residues: 1413 helix: 2.18 (0.18), residues: 807 sheet: 0.10 (0.53), residues: 92 loop : -0.98 (0.27), residues: 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.413 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.2978 time to fit residues: 37.5885 Evaluate side-chains 79 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1064 time to fit residues: 2.2090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11912 Z= 0.194 Angle : 0.487 9.527 16102 Z= 0.248 Chirality : 0.038 0.145 1835 Planarity : 0.004 0.054 2015 Dihedral : 4.859 66.804 1615 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.53 % 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: 1.46 (0.23), residues: 1413 helix: 2.23 (0.18), residues: 808 sheet: 0.03 (0.53), residues: 92 loop : -0.97 (0.27), residues: 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.530 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.3094 time to fit residues: 37.1515 Evaluate side-chains 81 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1231 time to fit residues: 2.9345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 HIS ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 11912 Z= 0.243 Angle : 0.507 9.649 16102 Z= 0.258 Chirality : 0.039 0.150 1835 Planarity : 0.004 0.051 2015 Dihedral : 4.932 66.514 1615 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.23), residues: 1413 helix: 2.20 (0.18), residues: 808 sheet: -0.08 (0.53), residues: 96 loop : -1.06 (0.27), residues: 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.451 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 86 average time/residue: 0.2996 time to fit residues: 36.5772 Evaluate side-chains 82 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1126 time to fit residues: 2.3968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11912 Z= 0.180 Angle : 0.474 10.127 16102 Z= 0.241 Chirality : 0.038 0.210 1835 Planarity : 0.004 0.049 2015 Dihedral : 4.814 65.606 1615 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.23 % 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: 1.47 (0.23), residues: 1413 helix: 2.27 (0.18), residues: 808 sheet: -0.04 (0.53), residues: 92 loop : -0.99 (0.27), residues: 513 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.508 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.3096 time to fit residues: 35.8285 Evaluate side-chains 81 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1096 time to fit residues: 2.3989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.0000 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11912 Z= 0.134 Angle : 0.457 10.297 16102 Z= 0.231 Chirality : 0.037 0.177 1835 Planarity : 0.003 0.048 2015 Dihedral : 4.689 64.194 1615 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.23 % 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: 1.58 (0.23), residues: 1413 helix: 2.35 (0.18), residues: 811 sheet: 0.01 (0.54), residues: 92 loop : -0.95 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.483 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.3200 time to fit residues: 39.3263 Evaluate side-chains 79 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1347 time to fit residues: 2.6357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1171 ASN L1554 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11912 Z= 0.203 Angle : 0.489 10.116 16102 Z= 0.247 Chirality : 0.038 0.148 1835 Planarity : 0.004 0.048 2015 Dihedral : 4.769 64.575 1615 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.23 % 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: 1.52 (0.23), residues: 1413 helix: 2.33 (0.18), residues: 809 sheet: -0.02 (0.53), residues: 96 loop : -1.03 (0.28), residues: 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.487 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 82 average time/residue: 0.3079 time to fit residues: 35.8682 Evaluate side-chains 79 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1110 time to fit residues: 2.4783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9980 chunk 120 optimal weight: 0.0570 chunk 128 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11912 Z= 0.140 Angle : 0.464 10.633 16102 Z= 0.234 Chirality : 0.037 0.141 1835 Planarity : 0.003 0.047 2015 Dihedral : 4.679 63.922 1615 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.00 % 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: 1.60 (0.23), residues: 1413 helix: 2.36 (0.18), residues: 811 sheet: 0.14 (0.59), residues: 82 loop : -0.95 (0.27), residues: 520 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.393 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3038 time to fit residues: 34.8368 Evaluate side-chains 80 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11912 Z= 0.155 Angle : 0.471 10.554 16102 Z= 0.238 Chirality : 0.037 0.163 1835 Planarity : 0.003 0.047 2015 Dihedral : 4.664 63.680 1615 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.15 % 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: 1.60 (0.23), residues: 1413 helix: 2.38 (0.18), residues: 811 sheet: -0.13 (0.55), residues: 92 loop : -0.94 (0.27), residues: 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.386 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.3000 time to fit residues: 35.6633 Evaluate side-chains 83 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1105 time to fit residues: 2.9658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 104 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 0.0020 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 overall best weight: 0.2926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN L 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057428 restraints weight = 64981.243| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.68 r_work: 0.2957 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11912 Z= 0.118 Angle : 0.457 10.668 16102 Z= 0.229 Chirality : 0.037 0.293 1835 Planarity : 0.003 0.047 2015 Dihedral : 4.573 62.925 1615 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.08 % 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: 1.71 (0.23), residues: 1413 helix: 2.43 (0.18), residues: 812 sheet: 0.19 (0.58), residues: 84 loop : -0.86 (0.27), residues: 517 =============================================================================== Job complete usr+sys time: 2418.79 seconds wall clock time: 45 minutes 3.02 seconds (2703.02 seconds total)