Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:07:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/11_2022/6v6c_21068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/11_2022/6v6c_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_21068/11_2022/6v6c_21068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/11_2022/6v6c_21068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/11_2022/6v6c_21068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6c_21068/11_2022/6v6c_21068.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral 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-4778/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: 2.76, per 1000 atoms: 0.69 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: 1.48 Conformation dependent library (CDL) restraints added in 672.8 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: 0.15 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: 0.94 Time building geometry restraints manager: 1.63 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 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. 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: 2.590 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: 9.400 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 % 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 *********************** 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 : 0.480 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1745 time to fit residues: 18.6450 Evaluate side-chains 62 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6441 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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: 0.8082 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4102 Z= 0.194 Angle : 0.561 8.093 5545 Z= 0.287 Chirality : 0.038 0.128 635 Planarity : 0.004 0.038 677 Dihedral : 4.469 18.952 529 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.38), residues: 471 helix: -1.15 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -2.40 (0.54), residues: 154 *********************** 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 90 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.496 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1318 time to fit residues: 15.5593 Evaluate side-chains 70 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5976 ------------------------------------------------------------------------------- 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: 0.0020 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1673 GLN ** L1679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1702 GLN ** L1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1759 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3100 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= 0.180 Angle : 0.543 8.021 5545 Z= 0.272 Chirality : 0.037 0.124 635 Planarity : 0.004 0.053 677 Dihedral : 4.322 18.954 529 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.40), residues: 471 helix: -0.54 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.36 (0.55), residues: 151 *********************** 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 83 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1318 time to fit residues: 14.4029 Evaluate side-chains 70 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6880 ------------------------------------------------------------------------------- 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: 0.6980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1508 HIS L1705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3431 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= 0.179 Angle : 0.544 7.906 5545 Z= 0.267 Chirality : 0.037 0.110 635 Planarity : 0.003 0.040 677 Dihedral : 4.266 18.772 529 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.41), residues: 471 helix: 0.00 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -2.40 (0.52), residues: 158 *********************** 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 84 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.487 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1427 time to fit residues: 15.6177 Evaluate side-chains 72 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8007 ------------------------------------------------------------------------------- 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: 0.0670 chunk 19 optimal weight: 0.2980 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 537 HIS L1571 ASN L1654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3913 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= 0.131 Angle : 0.517 7.897 5545 Z= 0.245 Chirality : 0.035 0.115 635 Planarity : 0.003 0.042 677 Dihedral : 4.022 17.919 529 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.42), residues: 471 helix: 0.23 (0.31), residues: 321 sheet: None (None), residues: 0 loop : -2.08 (0.56), residues: 150 *********************** 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 91 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.479 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1285 time to fit residues: 15.1759 Evaluate side-chains 70 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6435 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.4027 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= 0.166 Angle : 0.541 7.869 5545 Z= 0.264 Chirality : 0.037 0.109 635 Planarity : 0.003 0.041 677 Dihedral : 4.101 18.282 529 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.42), residues: 471 helix: 0.62 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -2.15 (0.55), residues: 158 *********************** 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 80 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.483 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1274 time to fit residues: 13.4931 Evaluate side-chains 65 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6540 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8063 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4102 Z= 0.206 Angle : 0.586 7.878 5545 Z= 0.287 Chirality : 0.038 0.138 635 Planarity : 0.003 0.040 677 Dihedral : 4.318 19.160 529 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.42), residues: 471 helix: 0.65 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.21 (0.54), residues: 157 *********************** 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 79 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.502 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1120 time to fit residues: 12.1486 Evaluate side-chains 62 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6468 ------------------------------------------------------------------------------- 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: 0.1980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 0.034 4102 Z= 0.175 Angle : 0.584 8.916 5545 Z= 0.284 Chirality : 0.038 0.133 635 Planarity : 0.003 0.041 677 Dihedral : 4.260 18.571 529 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.41), residues: 471 helix: 0.69 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.12 (0.55), residues: 155 *********************** 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 81 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.448 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1378 time to fit residues: 14.5873 Evaluate side-chains 61 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6554 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.0010 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1571 ASN L1639 HIS L1766 GLN L1770 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4304 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 : 0.593 7.735 5545 Z= 0.294 Chirality : 0.038 0.137 635 Planarity : 0.003 0.038 677 Dihedral : 4.281 19.308 529 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.46 % 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: -0.21 (0.41), residues: 471 helix: 0.80 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.11 (0.54), residues: 156 *********************** 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 79 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.486 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.1487 time to fit residues: 15.0834 Evaluate side-chains 60 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6575 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1571 ASN L1639 HIS L1770 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4310 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 : 0.601 7.859 5545 Z= 0.297 Chirality : 0.039 0.159 635 Planarity : 0.003 0.040 677 Dihedral : 4.315 20.263 529 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.41), residues: 471 helix: 0.83 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -1.97 (0.55), residues: 155 ********************** 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 78 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.486 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.1289 time to fit residues: 13.3832 Evaluate side-chains 59 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6601 ------------------------------------------------------------------------------- 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: 0.3980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1508 HIS L1568 HIS L1571 ASN L1639 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093552 restraints weight = 9900.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095270 restraints weight = 6079.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096485 restraints weight = 4159.750| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4408 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= 0.193 Angle : 0.614 7.748 5545 Z= 0.302 Chirality : 0.040 0.142 635 Planarity : 0.004 0.040 677 Dihedral : 4.365 21.798 529 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.41), residues: 471 helix: 0.84 (0.30), residues: 317 sheet: None (None), residues: 0 loop : -2.00 (0.54), residues: 154 =============================================================================== Job complete usr+sys time: 1169.82 seconds wall clock time: 22 minutes 6.13 seconds (1326.13 seconds total)