Starting phenix.real_space_refine on Sun Mar 10 18:32:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/03_2024/6v6c_21068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/03_2024/6v6c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/03_2024/6v6c_21068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/03_2024/6v6c_21068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/03_2024/6v6c_21068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/03_2024/6v6c_21068.pdb" } 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 Residue "L GLU 508": "OE1" <-> "OE2" Residue "L ARG 1478": "NH1" <-> "NH2" Residue "L GLU 1502": "OE1" <-> "OE2" Residue "L GLU 1510": "OE1" <-> "OE2" Residue "L ARG 1513": "NH1" <-> "NH2" Residue "L GLU 1533": "OE1" <-> "OE2" Residue "L GLU 1595": "OE1" <-> "OE2" Residue "L ARG 1801": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.55, per 1000 atoms: 0.64 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 - 3.50 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: 1.38 Conformation dependent library (CDL) restraints added in 953.0 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: 0.35 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: 0.92 Time building geometry restraints manager: 1.52 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: 100.20 - 106.96: 107 106.96 - 113.72: 2332 113.72 - 120.48: 1698 120.48 - 127.24: 1361 127.24 - 134.00: 47 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 2.440 nonbonded pdb=" O PHE L1780 " pdb=" OG1 THR L1784 " model vdw 2.237 2.440 nonbonded pdb=" O PHE L 429 " pdb=" OG1 THR L 433 " model vdw 2.262 2.440 nonbonded pdb=" O MET L1765 " pdb=" OG SER L1768 " model vdw 2.269 2.440 nonbonded pdb=" O ALA L 445 " pdb=" OG SER L 449 " model vdw 2.278 2.440 ... (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: 0.010 Normalize map: mean=0, sd=1: 2.050 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: 0.000 Extract box with map and model: 9.710 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.453 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: 0.1839 time to fit residues: 19.4948 Evaluate side-chains 65 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L1678 ASN L1679 GLN L1702 GLN ** L1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1777 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4102 Z= 0.181 Angle : 0.550 8.069 5545 Z= 0.281 Chirality : 0.038 0.127 635 Planarity : 0.004 0.039 677 Dihedral : 4.435 18.723 529 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.43 (0.38), residues: 471 helix: -1.14 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -2.37 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 539 HIS 0.004 0.001 HIS L1487 PHE 0.018 0.001 PHE L1688 TYR 0.008 0.001 TYR L1774 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 95 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8058 (tppp) cc_final: 0.7770 (ttpt) REVERT: L 530 GLU cc_start: 0.8499 (tp30) cc_final: 0.8021 (tm-30) REVERT: L 1493 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8535 (tmmt) REVERT: L 1510 GLU cc_start: 0.7011 (pt0) cc_final: 0.6427 (pt0) REVERT: L 1635 ASP cc_start: 0.8643 (t70) cc_final: 0.8420 (t70) REVERT: L 1703 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7737 (mmm-85) REVERT: L 1765 MET cc_start: 0.9194 (mtp) cc_final: 0.8951 (mtt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1582 time to fit residues: 18.6956 Evaluate side-chains 73 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.0000 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1702 GLN ** L1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1759 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2988 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= 0.186 Angle : 0.551 8.015 5545 Z= 0.277 Chirality : 0.038 0.155 635 Planarity : 0.004 0.051 677 Dihedral : 4.379 19.015 529 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % 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: -1.70 (0.40), residues: 471 helix: -0.50 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.34 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 539 HIS 0.004 0.001 HIS L1508 PHE 0.018 0.001 PHE L1638 TYR 0.008 0.001 TYR L 443 ARG 0.004 0.000 ARG L1597 *********************** 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 93 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: L 430 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8575 (tm-30) REVERT: L 464 LYS cc_start: 0.8213 (tppp) cc_final: 0.7983 (ttpt) REVERT: L 530 GLU cc_start: 0.8577 (tp30) cc_final: 0.8129 (tm-30) REVERT: L 1489 SER cc_start: 0.8913 (m) cc_final: 0.8652 (p) REVERT: L 1493 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8566 (tmmt) REVERT: L 1512 LEU cc_start: 0.9265 (pp) cc_final: 0.9058 (tt) REVERT: L 1529 ASP cc_start: 0.7885 (t70) cc_final: 0.7674 (t0) REVERT: L 1635 ASP cc_start: 0.8618 (t70) cc_final: 0.8397 (t70) REVERT: L 1673 GLN cc_start: 0.8845 (tt0) cc_final: 0.8242 (tm-30) REVERT: L 1703 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7597 (tpp80) REVERT: L 1765 MET cc_start: 0.9132 (mtp) cc_final: 0.8820 (mtt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1608 time to fit residues: 18.5500 Evaluate side-chains 75 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 ** L1766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3278 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= 0.194 Angle : 0.559 7.923 5545 Z= 0.275 Chirality : 0.038 0.141 635 Planarity : 0.004 0.040 677 Dihedral : 4.326 20.133 529 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -1.22 (0.41), residues: 471 helix: -0.02 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -2.34 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 539 HIS 0.005 0.001 HIS L1508 PHE 0.016 0.001 PHE L1638 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 87 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8357 (tppp) cc_final: 0.8038 (ttpt) REVERT: L 530 GLU cc_start: 0.8604 (tp30) cc_final: 0.8172 (tm-30) REVERT: L 1489 SER cc_start: 0.8935 (m) cc_final: 0.8596 (p) REVERT: L 1493 LYS cc_start: 0.9124 (mmtt) cc_final: 0.8592 (tmmt) REVERT: L 1518 MET cc_start: 0.8755 (tpp) cc_final: 0.8493 (tpp) REVERT: L 1703 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7525 (tpp80) REVERT: L 1765 MET cc_start: 0.9139 (mtp) cc_final: 0.8894 (mtt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1443 time to fit residues: 16.0199 Evaluate side-chains 72 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1571 ASN ** L1766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3486 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= 0.163 Angle : 0.542 7.886 5545 Z= 0.261 Chirality : 0.037 0.134 635 Planarity : 0.003 0.041 677 Dihedral : 4.181 19.925 529 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % 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: -0.81 (0.42), residues: 471 helix: 0.31 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -2.24 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 539 HIS 0.004 0.001 HIS L1508 PHE 0.012 0.001 PHE L1638 TYR 0.007 0.001 TYR L 443 ARG 0.004 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 85 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8388 (tppp) cc_final: 0.7954 (ttpt) REVERT: L 530 GLU cc_start: 0.8592 (tp30) cc_final: 0.8207 (tm-30) REVERT: L 1489 SER cc_start: 0.8945 (m) cc_final: 0.8614 (p) REVERT: L 1493 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8561 (tmmt) REVERT: L 1518 MET cc_start: 0.8760 (tpp) cc_final: 0.8426 (tpp) REVERT: L 1635 ASP cc_start: 0.8614 (t70) cc_final: 0.8314 (t0) REVERT: L 1703 ARG cc_start: 0.8361 (mtp180) cc_final: 0.7916 (tpp80) REVERT: L 1765 MET cc_start: 0.9150 (mtp) cc_final: 0.8947 (mtt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1355 time to fit residues: 14.9419 Evaluate side-chains 66 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 overall best weight: 0.3272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 537 HIS L1571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4102 Z= 0.137 Angle : 0.524 7.849 5545 Z= 0.253 Chirality : 0.036 0.122 635 Planarity : 0.003 0.042 677 Dihedral : 4.099 20.136 529 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.42 (0.42), residues: 471 helix: 0.60 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.07 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 539 HIS 0.003 0.001 HIS L1710 PHE 0.010 0.001 PHE L1638 TYR 0.017 0.001 TYR L1616 ARG 0.004 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 85 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7062 (tp30) REVERT: L 405 THR cc_start: 0.8327 (p) cc_final: 0.7646 (p) REVERT: L 430 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8570 (tm-30) REVERT: L 464 LYS cc_start: 0.8303 (tppp) cc_final: 0.7987 (ttpt) REVERT: L 530 GLU cc_start: 0.8578 (tp30) cc_final: 0.8238 (tm-30) REVERT: L 532 TYR cc_start: 0.8616 (t80) cc_final: 0.7862 (t80) REVERT: L 1489 SER cc_start: 0.8935 (m) cc_final: 0.8607 (p) REVERT: L 1493 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8498 (tmmt) REVERT: L 1703 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7965 (tpp80) REVERT: L 1765 MET cc_start: 0.9078 (mtp) cc_final: 0.8861 (mtt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1520 time to fit residues: 16.2853 Evaluate side-chains 67 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1571 ASN ** L1766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3690 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= 0.217 Angle : 0.583 7.891 5545 Z= 0.287 Chirality : 0.039 0.136 635 Planarity : 0.003 0.040 677 Dihedral : 4.309 19.312 529 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -0.46 (0.42), residues: 471 helix: 0.61 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.19 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 539 HIS 0.005 0.001 HIS L1508 PHE 0.013 0.001 PHE L1499 TYR 0.010 0.001 TYR L 443 ARG 0.002 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 fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8430 (tppp) cc_final: 0.8127 (ttpt) REVERT: L 530 GLU cc_start: 0.8632 (tp30) cc_final: 0.8219 (tm-30) REVERT: L 1489 SER cc_start: 0.8993 (m) cc_final: 0.8672 (p) REVERT: L 1493 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8561 (tmmt) REVERT: L 1703 ARG cc_start: 0.8465 (mtp180) cc_final: 0.7976 (tpp80) REVERT: L 1765 MET cc_start: 0.9219 (mtp) cc_final: 0.8888 (mtt) REVERT: L 1795 LEU cc_start: 0.9259 (tp) cc_final: 0.9051 (tt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1313 time to fit residues: 13.7705 Evaluate side-chains 64 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1571 ASN L1766 GLN L1770 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3826 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= 0.194 Angle : 0.568 7.893 5545 Z= 0.277 Chirality : 0.039 0.139 635 Planarity : 0.003 0.040 677 Dihedral : 4.294 20.137 529 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.23 % Allowed : 1.15 % Favored : 98.62 % 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: -0.35 (0.41), residues: 471 helix: 0.66 (0.31), residues: 317 sheet: None (None), residues: 0 loop : -2.12 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 539 HIS 0.004 0.001 HIS L1508 PHE 0.010 0.001 PHE L1499 TYR 0.008 0.001 TYR L 443 ARG 0.003 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 82 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8436 (tppp) cc_final: 0.8141 (ttpt) REVERT: L 530 GLU cc_start: 0.8622 (tp30) cc_final: 0.8225 (tm-30) REVERT: L 532 TYR cc_start: 0.8674 (t80) cc_final: 0.7863 (t80) REVERT: L 1489 SER cc_start: 0.9004 (m) cc_final: 0.8693 (p) REVERT: L 1493 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8538 (tmmt) REVERT: L 1703 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7844 (tpp80) REVERT: L 1765 MET cc_start: 0.9215 (mtp) cc_final: 0.8866 (mtt) REVERT: L 1766 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: L 1795 LEU cc_start: 0.9256 (tp) cc_final: 0.9052 (tt) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1416 time to fit residues: 14.9128 Evaluate side-chains 69 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1571 ASN L1770 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3926 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= 0.188 Angle : 0.573 7.843 5545 Z= 0.281 Chirality : 0.039 0.134 635 Planarity : 0.003 0.040 677 Dihedral : 4.274 19.611 529 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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: -0.30 (0.41), residues: 471 helix: 0.71 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.12 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 539 HIS 0.004 0.001 HIS L1508 PHE 0.011 0.001 PHE L1499 TYR 0.018 0.001 TYR L1616 ARG 0.003 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 78 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: L 464 LYS cc_start: 0.8431 (tppp) cc_final: 0.8143 (ttpt) REVERT: L 530 GLU cc_start: 0.8631 (tp30) cc_final: 0.8224 (tm-30) REVERT: L 532 TYR cc_start: 0.8670 (t80) cc_final: 0.7860 (t80) REVERT: L 1489 SER cc_start: 0.9002 (m) cc_final: 0.8698 (p) REVERT: L 1493 LYS cc_start: 0.9107 (mmtt) cc_final: 0.8589 (tmmt) REVERT: L 1703 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7861 (tpp80) REVERT: L 1765 MET cc_start: 0.9011 (mtp) cc_final: 0.8643 (mtm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1354 time to fit residues: 13.8241 Evaluate side-chains 60 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4091 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= 0.158 Angle : 0.560 7.766 5545 Z= 0.267 Chirality : 0.038 0.129 635 Planarity : 0.003 0.041 677 Dihedral : 4.129 20.140 529 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.86 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: -0.08 (0.42), residues: 471 helix: 0.91 (0.31), residues: 318 sheet: None (None), residues: 0 loop : -2.12 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 539 HIS 0.002 0.001 HIS L1508 PHE 0.011 0.001 PHE L1733 TYR 0.011 0.001 TYR L1616 ARG 0.003 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 80 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: L 402 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6884 (tp30) REVERT: L 405 THR cc_start: 0.8317 (p) cc_final: 0.7809 (p) REVERT: L 430 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8515 (tm-30) REVERT: L 464 LYS cc_start: 0.8346 (tppp) cc_final: 0.8079 (ttpt) REVERT: L 502 LEU cc_start: 0.9130 (tp) cc_final: 0.8628 (tp) REVERT: L 530 GLU cc_start: 0.8585 (tp30) cc_final: 0.8242 (tm-30) REVERT: L 532 TYR cc_start: 0.8649 (t80) cc_final: 0.7828 (t80) REVERT: L 1489 SER cc_start: 0.8993 (m) cc_final: 0.8686 (p) REVERT: L 1493 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8553 (tmmt) REVERT: L 1703 ARG cc_start: 0.8280 (mtp180) cc_final: 0.7845 (tpp80) REVERT: L 1765 MET cc_start: 0.8924 (mtp) cc_final: 0.8414 (mtt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1341 time to fit residues: 14.0521 Evaluate side-chains 68 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.103355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093588 restraints weight = 9939.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095412 restraints weight = 6199.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096656 restraints weight = 4272.834| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4017 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= 0.186 Angle : 0.572 7.791 5545 Z= 0.279 Chirality : 0.039 0.149 635 Planarity : 0.003 0.040 677 Dihedral : 4.228 19.526 529 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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: -0.07 (0.42), residues: 471 helix: 0.91 (0.31), residues: 319 sheet: None (None), residues: 0 loop : -2.14 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 539 HIS 0.003 0.001 HIS L1508 PHE 0.015 0.001 PHE L1733 TYR 0.012 0.001 TYR L1616 ARG 0.003 0.000 ARG L 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1261.45 seconds wall clock time: 23 minutes 21.75 seconds (1401.75 seconds total)