Starting phenix.real_space_refine on Wed Mar 5 23:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v6c_21068/03_2025/6v6c_21068.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v6c_21068/03_2025/6v6c_21068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2025/6v6c_21068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2025/6v6c_21068.map" model { file = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2025/6v6c_21068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v6c_21068/03_2025/6v6c_21068.cif" } resolution = 4.5 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2630 2.51 5 N 667 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4007 Number of models: 1 Model: "" Number of chains: 1 Chain: "L" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4007 Classifications: {'peptide': 497} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 479} Chain breaks: 12 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 3.69, per 1000 atoms: 0.92 Number of scatterers: 4007 At special positions: 0 Unit cell: (80.1, 77.43, 149.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 690 8.00 N 667 7.00 C 2630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 455.6 milliseconds 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 69.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'L' and resid 352 through 357 Processing helix chain 'L' and resid 392 through 412 removed outlier: 4.117A pdb=" N VAL L 400 " --> pdb=" O LEU L 396 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR L 403 " --> pdb=" O GLU L 399 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY L 404 " --> pdb=" O VAL L 400 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS L 406 " --> pdb=" O GLU L 402 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER L 411 " --> pdb=" O TYR L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.534A pdb=" N GLN L 430 " --> pdb=" O GLY L 426 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG L 437 " --> pdb=" O THR L 433 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG L 438 " --> pdb=" O SER L 434 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN L 441 " --> pdb=" O ARG L 437 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR L 442 " --> pdb=" O ARG L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 463 removed outlier: 3.540A pdb=" N ILE L 459 " --> pdb=" O SER L 455 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY L 460 " --> pdb=" O LEU L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 477 removed outlier: 4.841A pdb=" N GLN L 469 " --> pdb=" O LYS L 465 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA L 474 " --> pdb=" O LEU L 470 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU L 475 " --> pdb=" O ARG L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 512 removed outlier: 3.893A pdb=" N TYR L 506 " --> pdb=" O LEU L 502 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 509 " --> pdb=" O LEU L 505 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU L 510 " --> pdb=" O TYR L 506 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN L 512 " --> pdb=" O GLU L 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 529 removed outlier: 3.665A pdb=" N LEU L 521 " --> pdb=" O HIS L 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 540 removed outlier: 3.752A pdb=" N ARG L 534 " --> pdb=" O GLU L 530 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE L 535 " --> pdb=" O PRO L 531 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP L 539 " --> pdb=" O PHE L 535 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL L 540 " --> pdb=" O ILE L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 606 removed outlier: 3.615A pdb=" N ALA L 592 " --> pdb=" O LEU L 588 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS L 593 " --> pdb=" O LYS L 589 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP L 594 " --> pdb=" O HIS L 590 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 596 " --> pdb=" O ALA L 592 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 597 " --> pdb=" O HIS L 593 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS L 600 " --> pdb=" O TYR L 596 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE L 602 " --> pdb=" O CYS L 598 " (cutoff:3.500A) Processing helix chain 'L' and resid 1477 through 1504 removed outlier: 4.278A pdb=" N THR L1481 " --> pdb=" O LYS L1477 " (cutoff:3.500A) Proline residue: L1483 - end of helix removed outlier: 3.820A pdb=" N ALA L1486 " --> pdb=" O ALA L1482 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N HIS L1487 " --> pdb=" O PRO L1483 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER L1489 " --> pdb=" O ALA L1485 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU L1490 " --> pdb=" O ALA L1486 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE L1499 " --> pdb=" O ALA L1495 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU L1502 " --> pdb=" O TYR L1498 " (cutoff:3.500A) Processing helix chain 'L' and resid 1504 through 1516 removed outlier: 3.553A pdb=" N TYR L1509 " --> pdb=" O LEU L1505 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU L1510 " --> pdb=" O GLU L1506 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS L1514 " --> pdb=" O GLU L1510 " (cutoff:3.500A) Processing helix chain 'L' and resid 1523 through 1535 removed outlier: 4.333A pdb=" N ASP L1529 " --> pdb=" O GLN L1525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU L1533 " --> pdb=" O ASP L1529 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS L1534 " --> pdb=" O LEU L1530 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU L1535 " --> pdb=" O LEU L1531 " (cutoff:3.500A) Processing helix chain 'L' and resid 1552 through 1558 Processing helix chain 'L' and resid 1559 through 1562 removed outlier: 4.349A pdb=" N LEU L1562 " --> pdb=" O GLN L1559 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1559 through 1562' Processing helix chain 'L' and resid 1601 through 1606 removed outlier: 3.676A pdb=" N ILE L1606 " --> pdb=" O TRP L1602 " (cutoff:3.500A) Processing helix chain 'L' and resid 1611 through 1640 removed outlier: 3.987A pdb=" N PHE L1622 " --> pdb=" O GLY L1618 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L1629 " --> pdb=" O GLN L1625 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET L1630 " --> pdb=" O LEU L1626 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS L1634 " --> pdb=" O MET L1630 " (cutoff:3.500A) Processing helix chain 'L' and resid 1641 through 1644 Processing helix chain 'L' and resid 1652 through 1680 removed outlier: 3.549A pdb=" N LEU L1658 " --> pdb=" O GLN L1654 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE L1661 " --> pdb=" O GLN L1657 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS L1662 " --> pdb=" O LEU L1658 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS L1667 " --> pdb=" O HIS L1663 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE L1668 " --> pdb=" O GLU L1664 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL L1669 " --> pdb=" O MET L1665 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY L1674 " --> pdb=" O LYS L1670 " (cutoff:3.500A) Processing helix chain 'L' and resid 1682 through 1687 Processing helix chain 'L' and resid 1699 through 1715 removed outlier: 3.718A pdb=" N HIS L1710 " --> pdb=" O ALA L1706 " (cutoff:3.500A) Processing helix chain 'L' and resid 1722 through 1742 removed outlier: 3.557A pdb=" N MET L1726 " --> pdb=" O ALA L1722 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE L1729 " --> pdb=" O VAL L1725 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS L1730 " --> pdb=" O MET L1726 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER L1731 " --> pdb=" O ASN L1727 " (cutoff:3.500A) Processing helix chain 'L' and resid 1761 through 1785 removed outlier: 3.767A pdb=" N SER L1768 " --> pdb=" O LEU L1764 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS L1781 " --> pdb=" O HIS L1777 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR L1784 " --> pdb=" O PHE L1780 " (cutoff:3.500A) Processing helix chain 'L' and resid 1793 through 1803 removed outlier: 4.197A pdb=" N ASP L1797 " --> pdb=" O PRO L1793 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE L1798 " --> pdb=" O HIS L1794 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU L1799 " --> pdb=" O LEU L1795 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU L1800 " --> pdb=" O GLU L1796 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 546 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: 0.89 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1232 1.35 - 1.46: 1038 1.46 - 1.58: 1804 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 4102 Sorted by residual: bond pdb=" N VAL L 353 " pdb=" CA VAL L 353 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.81e+00 bond pdb=" N LYS L 354 " pdb=" CA LYS L 354 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.35e-02 5.49e+03 4.93e+00 bond pdb=" N LEU L 352 " pdb=" CA LEU L 352 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.77e-02 3.19e+03 4.87e+00 bond pdb=" N GLU L 351 " pdb=" CA GLU L 351 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" C GLU L 351 " pdb=" N LEU L 352 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.35e-02 5.49e+03 9.67e-01 ... (remaining 4097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 5453 1.63 - 3.27: 72 3.27 - 4.90: 14 4.90 - 6.54: 4 6.54 - 8.17: 2 Bond angle restraints: 5545 Sorted by residual: angle pdb=" O VAL L 353 " pdb=" C VAL L 353 " pdb=" N LYS L 354 " ideal model delta sigma weight residual 121.83 124.65 -2.82 1.03e+00 9.43e-01 7.48e+00 angle pdb=" N VAL L1783 " pdb=" CA VAL L1783 " pdb=" C VAL L1783 " ideal model delta sigma weight residual 111.00 108.25 2.75 1.09e+00 8.42e-01 6.37e+00 angle pdb=" N LYS L 354 " pdb=" CA LYS L 354 " pdb=" C LYS L 354 " ideal model delta sigma weight residual 113.01 110.06 2.95 1.20e+00 6.94e-01 6.06e+00 angle pdb=" CA VAL L 353 " pdb=" C VAL L 353 " pdb=" O VAL L 353 " ideal model delta sigma weight residual 120.85 118.34 2.51 1.06e+00 8.90e-01 5.63e+00 angle pdb=" CA LEU L 567 " pdb=" CB LEU L 567 " pdb=" CG LEU L 567 " ideal model delta sigma weight residual 116.30 124.47 -8.17 3.50e+00 8.16e-02 5.45e+00 ... (remaining 5540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 2122 16.16 - 32.31: 238 32.31 - 48.47: 38 48.47 - 64.63: 5 64.63 - 80.79: 5 Dihedral angle restraints: 2408 sinusoidal: 946 harmonic: 1462 Sorted by residual: dihedral pdb=" CA ASP L1601 " pdb=" C ASP L1601 " pdb=" N TRP L1602 " pdb=" CA TRP L1602 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA CYS L1686 " pdb=" C CYS L1686 " pdb=" N GLU L1687 " pdb=" CA GLU L1687 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PRO L 451 " pdb=" C PRO L 451 " pdb=" N PRO L 452 " pdb=" CA PRO L 452 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 2405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 363 0.030 - 0.060: 207 0.060 - 0.090: 48 0.090 - 0.120: 16 0.120 - 0.151: 1 Chirality restraints: 635 Sorted by residual: chirality pdb=" CA VAL L 353 " pdb=" N VAL L 353 " pdb=" C VAL L 353 " pdb=" CB VAL L 353 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE L1608 " pdb=" N ILE L1608 " pdb=" C ILE L1608 " pdb=" CB ILE L1608 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CB VAL L 353 " pdb=" CA VAL L 353 " pdb=" CG1 VAL L 353 " pdb=" CG2 VAL L 353 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.11 2.00e-01 2.50e+01 2.99e-01 ... (remaining 632 not shown) Planarity restraints: 677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 351 " 0.011 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C GLU L 351 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU L 351 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU L 352 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L1566 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO L1567 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO L1567 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L1567 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN L1546 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO L1547 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO L1547 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO L1547 " -0.014 5.00e-02 4.00e+02 ... (remaining 674 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 764 2.76 - 3.30: 3974 3.30 - 3.83: 5824 3.83 - 4.37: 6758 4.37 - 4.90: 10621 Nonbonded interactions: 27941 Sorted by model distance: nonbonded pdb=" O GLY L1611 " pdb=" OG SER L1614 " model vdw 2.226 3.040 nonbonded pdb=" O PHE L1780 " pdb=" OG1 THR L1784 " model vdw 2.237 3.040 nonbonded pdb=" O PHE L 429 " pdb=" OG1 THR L 433 " model vdw 2.262 3.040 nonbonded pdb=" O MET L1765 " pdb=" OG SER L1768 " model vdw 2.269 3.040 nonbonded pdb=" O ALA L 445 " pdb=" OG SER L 449 " model vdw 2.278 3.040 ... (remaining 27936 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.080 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.003 0.039 4102 Z= 0.210 Angle : 0.547 8.172 5545 Z= 0.297 Chirality : 0.038 0.151 635 Planarity : 0.003 0.029 677 Dihedral : 13.781 80.787 1456 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % 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: -4.56 (0.32), residues: 471 helix: -2.93 (0.22), residues: 302 sheet: None (None), residues: 0 loop : -2.89 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L1685 HIS 0.003 0.001 HIS L1710 PHE 0.009 0.001 PHE L 552 TYR 0.007 0.001 TYR L 443 ARG 0.001 0.000 ARG L 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8210 (tppp) cc_final: 0.7704 (ttpt) REVERT: L 530 GLU cc_start: 0.8772 (tp30) cc_final: 0.8160 (tm-30) REVERT: L 1493 LYS cc_start: 0.9342 (mmtt) cc_final: 0.8685 (tmmt) REVERT: L 1638 PHE cc_start: 0.8232 (t80) cc_final: 0.7893 (t80) REVERT: L 1703 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7817 (mtm180) REVERT: L 1765 MET cc_start: 0.9222 (mtp) cc_final: 0.8905 (mtt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1854 time to fit residues: 19.7226 Evaluate side-chains 65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 517 HIS L1559 GLN L1673 GLN L1702 GLN ** L1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092188 restraints weight = 9792.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093949 restraints weight = 6141.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095182 restraints weight = 4244.447| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4102 Z= 0.191 Angle : 0.571 8.458 5545 Z= 0.293 Chirality : 0.038 0.127 635 Planarity : 0.004 0.040 677 Dihedral : 4.479 19.090 529 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.23 % Allowed : 5.28 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.50 (0.38), residues: 471 helix: -1.15 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 539 HIS 0.003 0.001 HIS L1777 PHE 0.020 0.001 PHE L1688 TYR 0.009 0.001 TYR L 443 ARG 0.004 0.000 ARG L1597 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8017 (tppp) cc_final: 0.7788 (ttpt) REVERT: L 530 GLU cc_start: 0.8585 (tp30) cc_final: 0.8111 (tm-30) REVERT: L 1493 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8583 (tmmt) REVERT: L 1510 GLU cc_start: 0.6776 (pt0) cc_final: 0.6279 (pt0) REVERT: L 1630 MET cc_start: 0.8215 (mtp) cc_final: 0.7961 (mtp) REVERT: L 1673 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: L 1689 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.7803 (mmm-85) REVERT: L 1702 GLN cc_start: 0.8348 (mt0) cc_final: 0.8099 (mt0) REVERT: L 1703 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7819 (mmm-85) REVERT: L 1765 MET cc_start: 0.9193 (mtp) cc_final: 0.8940 (mtt) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1724 time to fit residues: 20.4657 Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 0.0050 chunk 27 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1625 GLN ** L1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1759 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095007 restraints weight = 9688.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096866 restraints weight = 5968.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098200 restraints weight = 4069.428| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4102 Z= 0.166 Angle : 0.535 8.414 5545 Z= 0.267 Chirality : 0.037 0.119 635 Planarity : 0.004 0.053 677 Dihedral : 4.279 18.845 529 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: -1.79 (0.40), residues: 471 helix: -0.56 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -2.41 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 539 HIS 0.004 0.001 HIS L1508 PHE 0.010 0.001 PHE L1688 TYR 0.008 0.001 TYR L1616 ARG 0.005 0.000 ARG L 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7106 (tp30) REVERT: L 430 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8556 (tm-30) REVERT: L 530 GLU cc_start: 0.8644 (tp30) cc_final: 0.8241 (tm-30) REVERT: L 600 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8945 (mtmm) REVERT: L 1489 SER cc_start: 0.8896 (m) cc_final: 0.8630 (p) REVERT: L 1493 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8614 (tmmt) REVERT: L 1703 ARG cc_start: 0.8072 (mtp180) cc_final: 0.7626 (tpp80) REVERT: L 1765 MET cc_start: 0.9153 (mtp) cc_final: 0.8919 (mtt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1595 time to fit residues: 19.1332 Evaluate side-chains 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1508 HIS L1571 ASN L1705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094868 restraints weight = 9837.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096584 restraints weight = 6184.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097776 restraints weight = 4282.738| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4102 Z= 0.171 Angle : 0.542 8.413 5545 Z= 0.267 Chirality : 0.037 0.110 635 Planarity : 0.004 0.042 677 Dihedral : 4.179 19.005 529 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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: -1.30 (0.40), residues: 471 helix: -0.03 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.51 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 539 HIS 0.004 0.001 HIS L1508 PHE 0.011 0.001 PHE L1499 TYR 0.008 0.001 TYR L 443 ARG 0.005 0.000 ARG L 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7017 (tp30) REVERT: L 530 GLU cc_start: 0.8629 (tp30) cc_final: 0.8233 (tm-30) REVERT: L 600 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8883 (mtmm) REVERT: L 1489 SER cc_start: 0.8990 (m) cc_final: 0.8628 (p) REVERT: L 1493 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8640 (tmmt) REVERT: L 1703 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7785 (tpp80) REVERT: L 1765 MET cc_start: 0.9098 (mtp) cc_final: 0.8878 (mtt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1627 time to fit residues: 17.6144 Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 0.0470 chunk 28 optimal weight: 0.0270 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095691 restraints weight = 10077.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097434 restraints weight = 6253.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098648 restraints weight = 4282.807| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4102 Z= 0.155 Angle : 0.548 8.368 5545 Z= 0.263 Chirality : 0.037 0.131 635 Planarity : 0.003 0.042 677 Dihedral : 4.094 18.623 529 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -0.92 (0.41), residues: 471 helix: 0.26 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.38 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 539 HIS 0.003 0.001 HIS L1508 PHE 0.007 0.001 PHE L 495 TYR 0.013 0.001 TYR L1616 ARG 0.006 0.000 ARG L 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7011 (tp30) REVERT: L 530 GLU cc_start: 0.8632 (tp30) cc_final: 0.8296 (tm-30) REVERT: L 600 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8866 (mtmm) REVERT: L 1489 SER cc_start: 0.8940 (m) cc_final: 0.8574 (p) REVERT: L 1493 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8585 (tmmt) REVERT: L 1518 MET cc_start: 0.8839 (tpp) cc_final: 0.8592 (tpp) REVERT: L 1689 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.7722 (mmm-85) REVERT: L 1703 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7741 (tpp80) REVERT: L 1765 MET cc_start: 0.9073 (mtp) cc_final: 0.8771 (mtt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1503 time to fit residues: 16.4552 Evaluate side-chains 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 15 optimal weight: 0.0470 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1568 HIS L1571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096749 restraints weight = 9797.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098432 restraints weight = 6121.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099668 restraints weight = 4237.186| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4102 Z= 0.141 Angle : 0.519 7.687 5545 Z= 0.252 Chirality : 0.037 0.138 635 Planarity : 0.003 0.042 677 Dihedral : 4.021 18.202 529 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -0.52 (0.42), residues: 471 helix: 0.50 (0.31), residues: 318 sheet: None (None), residues: 0 loop : -2.12 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 539 HIS 0.002 0.000 HIS L1508 PHE 0.010 0.001 PHE L1733 TYR 0.006 0.001 TYR L 443 ARG 0.006 0.000 ARG L 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7105 (tp30) REVERT: L 430 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8475 (tm-30) REVERT: L 502 LEU cc_start: 0.9021 (tp) cc_final: 0.8494 (tp) REVERT: L 530 GLU cc_start: 0.8648 (tp30) cc_final: 0.8340 (tm-30) REVERT: L 532 TYR cc_start: 0.8697 (t80) cc_final: 0.7881 (t80) REVERT: L 600 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8791 (mtmm) REVERT: L 1489 SER cc_start: 0.8955 (m) cc_final: 0.8605 (p) REVERT: L 1493 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8519 (tmmt) REVERT: L 1689 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7654 (mmm-85) REVERT: L 1703 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7736 (tpp80) REVERT: L 1765 MET cc_start: 0.9071 (mtp) cc_final: 0.8794 (mtt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1477 time to fit residues: 15.5470 Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1568 HIS L1571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094530 restraints weight = 9974.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096306 restraints weight = 6205.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097493 restraints weight = 4244.223| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4102 Z= 0.182 Angle : 0.571 7.320 5545 Z= 0.281 Chirality : 0.039 0.152 635 Planarity : 0.003 0.042 677 Dihedral : 4.177 19.671 529 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -0.47 (0.41), residues: 471 helix: 0.52 (0.31), residues: 319 sheet: None (None), residues: 0 loop : -2.07 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 539 HIS 0.004 0.001 HIS L1504 PHE 0.022 0.001 PHE L1499 TYR 0.013 0.001 TYR L1616 ARG 0.006 0.000 ARG L 534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7101 (tp30) REVERT: L 502 LEU cc_start: 0.9092 (tp) cc_final: 0.8536 (tp) REVERT: L 530 GLU cc_start: 0.8680 (tp30) cc_final: 0.8312 (tm-30) REVERT: L 532 TYR cc_start: 0.8728 (t80) cc_final: 0.7893 (t80) REVERT: L 600 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8834 (mtmm) REVERT: L 1489 SER cc_start: 0.8964 (m) cc_final: 0.8628 (p) REVERT: L 1493 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8610 (tmmt) REVERT: L 1689 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7630 (mmm-85) REVERT: L 1703 ARG cc_start: 0.8240 (mtp180) cc_final: 0.7736 (tpp80) REVERT: L 1765 MET cc_start: 0.9131 (mtp) cc_final: 0.8870 (mtt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1659 time to fit residues: 16.6235 Evaluate side-chains 64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1568 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096881 restraints weight = 9789.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098577 restraints weight = 6188.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099716 restraints weight = 4297.154| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4102 Z= 0.157 Angle : 0.549 7.200 5545 Z= 0.265 Chirality : 0.037 0.139 635 Planarity : 0.003 0.043 677 Dihedral : 4.075 19.057 529 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -0.20 (0.41), residues: 471 helix: 0.83 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -2.10 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 539 HIS 0.001 0.000 HIS L1508 PHE 0.009 0.001 PHE L1733 TYR 0.009 0.001 TYR L1616 ARG 0.007 0.000 ARG L 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: L 397 LEU cc_start: 0.9420 (tp) cc_final: 0.9207 (tp) REVERT: L 402 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6995 (tp30) REVERT: L 502 LEU cc_start: 0.9022 (tp) cc_final: 0.8539 (tp) REVERT: L 530 GLU cc_start: 0.8632 (tp30) cc_final: 0.8331 (tm-30) REVERT: L 532 TYR cc_start: 0.8708 (t80) cc_final: 0.7894 (t80) REVERT: L 600 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8803 (mtmm) REVERT: L 1489 SER cc_start: 0.8945 (m) cc_final: 0.8592 (p) REVERT: L 1493 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8689 (tmmt) REVERT: L 1689 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7638 (mmm-85) REVERT: L 1703 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7600 (tpp80) REVERT: L 1765 MET cc_start: 0.9104 (mtp) cc_final: 0.8724 (mtt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1540 time to fit residues: 16.6729 Evaluate side-chains 75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 32 optimal weight: 0.0030 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099249 restraints weight = 9840.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101035 restraints weight = 6083.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102278 restraints weight = 4142.102| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4102 Z= 0.143 Angle : 0.568 6.963 5545 Z= 0.265 Chirality : 0.038 0.129 635 Planarity : 0.003 0.042 677 Dihedral : 3.979 19.967 529 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.03 (0.42), residues: 471 helix: 0.96 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -1.92 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 539 HIS 0.003 0.000 HIS L1508 PHE 0.020 0.001 PHE L1688 TYR 0.007 0.001 TYR L1616 ARG 0.007 0.000 ARG L 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6887 (tp30) REVERT: L 430 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8510 (tm-30) REVERT: L 502 LEU cc_start: 0.9024 (tp) cc_final: 0.8625 (tp) REVERT: L 530 GLU cc_start: 0.8641 (tp30) cc_final: 0.8378 (tm-30) REVERT: L 532 TYR cc_start: 0.8643 (t80) cc_final: 0.7997 (t80) REVERT: L 600 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8793 (mtmm) REVERT: L 1489 SER cc_start: 0.8933 (m) cc_final: 0.8573 (p) REVERT: L 1493 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8649 (tmmt) REVERT: L 1639 HIS cc_start: 0.8331 (t70) cc_final: 0.7922 (t-170) REVERT: L 1689 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7549 (mmm-85) REVERT: L 1703 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7596 (tpp80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1607 time to fit residues: 18.5051 Evaluate side-chains 73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095383 restraints weight = 9917.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097135 restraints weight = 6138.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098369 restraints weight = 4202.436| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4102 Z= 0.173 Angle : 0.591 7.029 5545 Z= 0.281 Chirality : 0.039 0.139 635 Planarity : 0.003 0.042 677 Dihedral : 4.072 19.392 529 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.09 (0.42), residues: 471 helix: 0.91 (0.31), residues: 319 sheet: None (None), residues: 0 loop : -1.77 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 539 HIS 0.002 0.001 HIS L1705 PHE 0.019 0.001 PHE L1688 TYR 0.009 0.001 TYR L1616 ARG 0.006 0.000 ARG L 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 942 Ramachandran restraints generated. 471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7000 (tp30) REVERT: L 430 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8526 (tm-30) REVERT: L 502 LEU cc_start: 0.9112 (tp) cc_final: 0.8664 (tp) REVERT: L 530 GLU cc_start: 0.8674 (tp30) cc_final: 0.8324 (tm-30) REVERT: L 532 TYR cc_start: 0.8677 (t80) cc_final: 0.7938 (t80) REVERT: L 600 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8815 (mtmm) REVERT: L 1489 SER cc_start: 0.8956 (m) cc_final: 0.8610 (p) REVERT: L 1493 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8624 (tmmt) REVERT: L 1639 HIS cc_start: 0.8311 (t70) cc_final: 0.7933 (t-170) REVERT: L 1689 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7639 (mmm-85) REVERT: L 1703 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7660 (tpp80) REVERT: L 1735 LEU cc_start: 0.9314 (mt) cc_final: 0.9112 (mt) REVERT: L 1795 LEU cc_start: 0.9087 (tp) cc_final: 0.8875 (tt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1699 time to fit residues: 18.1292 Evaluate side-chains 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1504 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.092548 restraints weight = 9892.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094255 restraints weight = 6156.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095450 restraints weight = 4237.437| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4102 Z= 0.222 Angle : 0.643 7.091 5545 Z= 0.313 Chirality : 0.040 0.127 635 Planarity : 0.004 0.040 677 Dihedral : 4.397 21.277 529 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.10 (0.41), residues: 471 helix: 0.79 (0.31), residues: 320 sheet: None (None), residues: 0 loop : -1.90 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 539 HIS 0.006 0.001 HIS L1504 PHE 0.019 0.001 PHE L1688 TYR 0.009 0.001 TYR L 443 ARG 0.006 0.001 ARG L 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.14 seconds wall clock time: 29 minutes 53.07 seconds (1793.07 seconds total)