Starting phenix.real_space_refine on Fri Mar 15 03:42:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7r_33046/03_2024/7x7r_33046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7r_33046/03_2024/7x7r_33046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7r_33046/03_2024/7x7r_33046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7r_33046/03_2024/7x7r_33046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7r_33046/03_2024/7x7r_33046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7r_33046/03_2024/7x7r_33046.pdb" } resolution = 3.5 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= 1.000 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 56 5.49 5 S 31 5.16 5 C 6510 2.51 5 N 1854 2.21 5 O 2074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10529 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 758 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "J" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 436 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "A" Number of atoms: 9335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1241, 9335 Unusual residues: {' ZN': 4} Classifications: {'peptide': 1237, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 59, 'TRANS': 1177, None: 4} Not linked: pdbres="ASN A1689 " pdbres=" ZN A1801 " Not linked: pdbres=" ZN A1801 " pdbres=" ZN A1802 " Not linked: pdbres=" ZN A1802 " pdbres=" ZN A1803 " Not linked: pdbres=" ZN A1803 " pdbres=" ZN A1804 " Chain breaks: 9 Unresolved non-hydrogen bonds: 662 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 25, 'TYR:plan': 1, 'ASN:plan1': 19, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 42, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 427 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4549 SG CYS A 491 21.330 25.347 102.757 1.00 39.67 S ATOM 4631 SG CYS A 503 21.864 25.027 104.149 1.00 40.30 S ATOM 4653 SG CYS A 506 24.237 26.584 103.898 1.00 34.60 S ATOM 1852 SG CYS A 88 28.779 35.019 134.217 1.00 54.56 S ATOM 2090 SG CYS A 121 27.754 36.202 137.716 1.00 80.87 S ATOM 2121 SG CYS A 127 31.434 36.295 136.707 1.00 63.26 S ATOM 2145 SG CYS A 130 28.979 38.632 135.016 1.00 57.48 S ATOM 6514 SG CYS A 750 12.128 24.187 73.080 1.00 80.94 S ATOM 6527 SG CYS A 752 15.322 22.825 71.640 1.00 66.35 S ATOM 6549 SG CYS A 755 15.557 24.790 74.873 1.00 52.19 S ATOM 8530 SG CYS A1406 19.111 40.825 43.697 1.00 53.55 S ATOM 8581 SG CYS A1414 18.032 40.581 41.695 1.00 43.81 S ATOM 8598 SG CYS A1417 21.390 39.108 43.424 1.00 39.10 S Time building chain proxies: 6.37, per 1000 atoms: 0.60 Number of scatterers: 10529 At special positions: 0 Unit cell: (73.1499, 84.5499, 152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 31 16.00 P 56 15.00 O 2074 8.00 N 1854 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " Number of angles added : 9 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 29.0% alpha, 15.0% beta 5 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.282A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.011A pdb=" N MET A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.516A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.648A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.677A pdb=" N ILE A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.276A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.761A pdb=" N ARG A 510 " --> pdb=" O CYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.795A pdb=" N ARG A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.577A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.999A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.820A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 removed outlier: 3.567A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 657' Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.791A pdb=" N LYS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 removed outlier: 3.527A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.508A pdb=" N ILE A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.515A pdb=" N VAL A 858 " --> pdb=" O LYS A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.824A pdb=" N GLU A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.741A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.823A pdb=" N LEU A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 removed outlier: 3.500A pdb=" N LEU A1419 " --> pdb=" O PRO A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.341A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.801A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1499 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.847A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A1534 " --> pdb=" O TRP A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1599 removed outlier: 4.103A pdb=" N GLY A1594 " --> pdb=" O TYR A1590 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A1599 " --> pdb=" O TYR A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.602A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 removed outlier: 3.815A pdb=" N LYS A1624 " --> pdb=" O PRO A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.661A pdb=" N VAL A1678 " --> pdb=" O TYR A1674 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A1679 " --> pdb=" O LYS A1675 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 158 removed outlier: 5.527A pdb=" N PHE A 153 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR A 210 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN A 155 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 208 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 238 " --> pdb=" O GLU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.012A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.889A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 513 removed outlier: 6.732A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 534 removed outlier: 5.884A pdb=" N SER A 544 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ASN A 534 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N ASP A 542 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.823A pdb=" N ARG A 768 " --> pdb=" O TRP A 825 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.627A pdb=" N GLU A 677 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 865 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 925 through 927 Processing sheet with id=AB2, first strand: chain 'A' and resid 950 through 952 removed outlier: 7.224A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1430 through 1431 removed outlier: 6.773A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 985 through 986 removed outlier: 6.201A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 992 277 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2879 1.33 - 1.45: 2252 1.45 - 1.57: 5606 1.57 - 1.69: 110 1.69 - 1.81: 42 Bond restraints: 10889 Sorted by residual: bond pdb=" N1 C J 23 " pdb=" C2 C J 23 " ideal model delta sigma weight residual 1.397 1.419 -0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C3' A J 19 " pdb=" O3' A J 19 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.19e+00 bond pdb=" N PHE A 24 " pdb=" CA PHE A 24 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.88e-01 bond pdb=" O3' A J 19 " pdb=" P G J 20 " ideal model delta sigma weight residual 1.607 1.618 -0.011 1.50e-02 4.44e+03 5.51e-01 bond pdb=" N ASP A 400 " pdb=" CA ASP A 400 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.54e-02 4.22e+03 5.40e-01 ... (remaining 10884 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.84: 489 105.84 - 112.90: 5827 112.90 - 119.97: 3703 119.97 - 127.04: 4763 127.04 - 134.10: 254 Bond angle restraints: 15036 Sorted by residual: angle pdb=" C3' A J 19 " pdb=" O3' A J 19 " pdb=" P G J 20 " ideal model delta sigma weight residual 120.20 125.16 -4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" N VAL A1618 " pdb=" CA VAL A1618 " pdb=" C VAL A1618 " ideal model delta sigma weight residual 112.29 109.52 2.77 9.40e-01 1.13e+00 8.68e+00 angle pdb=" C1' C J 23 " pdb=" N1 C J 23 " pdb=" C2 C J 23 " ideal model delta sigma weight residual 118.80 127.12 -8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" C PHE A 780 " pdb=" N GLU A 781 " pdb=" CA GLU A 781 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.63e+00 angle pdb=" C PHE A 24 " pdb=" CA PHE A 24 " pdb=" CB PHE A 24 " ideal model delta sigma weight residual 110.42 115.78 -5.36 1.99e+00 2.53e-01 7.26e+00 ... (remaining 15031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 6210 35.18 - 70.36: 249 70.36 - 105.53: 32 105.53 - 140.71: 0 140.71 - 175.89: 5 Dihedral angle restraints: 6496 sinusoidal: 2968 harmonic: 3528 Sorted by residual: dihedral pdb=" O4' U C -14 " pdb=" C1' U C -14 " pdb=" N1 U C -14 " pdb=" C2 U C -14 " ideal model delta sinusoidal sigma weight residual 200.00 58.81 141.19 1 1.50e+01 4.44e-03 7.59e+01 dihedral pdb=" O4' U J 36 " pdb=" C1' U J 36 " pdb=" N1 U J 36 " pdb=" C2 U J 36 " ideal model delta sinusoidal sigma weight residual 232.00 56.11 175.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual -128.00 47.38 -175.38 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 6493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1363 0.046 - 0.091: 262 0.091 - 0.137: 70 0.137 - 0.182: 5 0.182 - 0.228: 1 Chirality restraints: 1701 Sorted by residual: chirality pdb=" CB ILE A1468 " pdb=" CA ILE A1468 " pdb=" CG1 ILE A1468 " pdb=" CG2 ILE A1468 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' A J 19 " pdb=" C4' A J 19 " pdb=" O3' A J 19 " pdb=" C2' A J 19 " both_signs ideal model delta sigma weight residual False -2.74 -2.58 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" C1' U C -14 " pdb=" O4' U C -14 " pdb=" C2' U C -14 " pdb=" N1 U C -14 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1698 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1475 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A1476 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1476 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1476 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 316 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 317 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 1 " 0.017 2.00e-02 2.50e+03 9.94e-03 2.22e+00 pdb=" N1 C C 1 " -0.024 2.00e-02 2.50e+03 pdb=" C2 C C 1 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C C 1 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C C 1 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C C 1 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C C 1 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C C 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C C 1 " -0.001 2.00e-02 2.50e+03 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 154 2.63 - 3.19: 9366 3.19 - 3.76: 16766 3.76 - 4.33: 22090 4.33 - 4.90: 35754 Nonbonded interactions: 84130 Sorted by model distance: nonbonded pdb=" O2' U C 5 " pdb=" O ALA A 685 " model vdw 2.058 2.440 nonbonded pdb=" O LEU A1648 " pdb=" OG1 THR A1662 " model vdw 2.217 2.440 nonbonded pdb=" OG SER A 680 " pdb=" O GLY A 859 " model vdw 2.263 2.440 nonbonded pdb=" O2' G J 20 " pdb=" O4' U J 21 " model vdw 2.263 2.440 nonbonded pdb=" NH2 ARG A 737 " pdb=" OE1 GLU A1525 " model vdw 2.264 2.520 ... (remaining 84125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 6.160 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.750 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 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 : 0.002 0.035 10889 Z= 0.134 Angle : 0.584 8.316 15036 Z= 0.291 Chirality : 0.040 0.228 1701 Planarity : 0.003 0.043 1726 Dihedral : 18.553 175.890 4236 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1217 helix: 0.20 (0.32), residues: 292 sheet: -0.80 (0.42), residues: 170 loop : -1.22 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 862 HIS 0.004 0.001 HIS A 33 PHE 0.023 0.001 PHE A 546 TYR 0.018 0.001 TYR A 649 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.6243 (tmm) cc_final: 0.5741 (tmm) REVERT: A 191 TYR cc_start: 0.6919 (p90) cc_final: 0.6715 (p90) REVERT: A 627 MET cc_start: 0.7202 (mtt) cc_final: 0.6970 (mtt) REVERT: A 760 ASN cc_start: 0.7368 (p0) cc_final: 0.7138 (p0) REVERT: A 1004 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7184 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2413 time to fit residues: 54.6035 Evaluate side-chains 114 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.0030 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10889 Z= 0.231 Angle : 0.586 7.847 15036 Z= 0.297 Chirality : 0.042 0.316 1701 Planarity : 0.004 0.042 1726 Dihedral : 19.437 177.165 2200 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 1.89 % Allowed : 10.89 % Favored : 87.22 % 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: -1.38 (0.25), residues: 1217 helix: 0.11 (0.30), residues: 308 sheet: -0.99 (0.40), residues: 176 loop : -1.38 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 862 HIS 0.005 0.001 HIS A 924 PHE 0.022 0.001 PHE A 824 TYR 0.022 0.002 TYR A 199 ARG 0.004 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.035 Fit side-chains REVERT: A 627 MET cc_start: 0.7254 (mtt) cc_final: 0.7031 (mtt) REVERT: A 1004 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7551 (tpp-160) outliers start: 17 outliers final: 10 residues processed: 151 average time/residue: 0.2138 time to fit residues: 45.8583 Evaluate side-chains 129 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 126 optimal weight: 0.0030 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10889 Z= 0.148 Angle : 0.550 11.104 15036 Z= 0.273 Chirality : 0.041 0.301 1701 Planarity : 0.004 0.059 1726 Dihedral : 19.351 175.855 2200 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.00 % Allowed : 15.22 % Favored : 82.78 % 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: -1.24 (0.25), residues: 1217 helix: 0.29 (0.31), residues: 308 sheet: -0.90 (0.41), residues: 178 loop : -1.32 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1530 HIS 0.004 0.001 HIS A 924 PHE 0.028 0.001 PHE A 226 TYR 0.016 0.001 TYR A 649 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.022 Fit side-chains REVERT: A 472 ARG cc_start: 0.6938 (tmm-80) cc_final: 0.6533 (tmm160) REVERT: A 627 MET cc_start: 0.7258 (mtt) cc_final: 0.7009 (mtt) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.2464 time to fit residues: 52.0380 Evaluate side-chains 136 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 43 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10889 Z= 0.188 Angle : 0.562 12.463 15036 Z= 0.279 Chirality : 0.041 0.326 1701 Planarity : 0.004 0.060 1726 Dihedral : 19.369 176.608 2200 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.00 % Allowed : 17.56 % Favored : 79.44 % 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: -1.23 (0.25), residues: 1217 helix: 0.38 (0.31), residues: 302 sheet: -0.80 (0.41), residues: 178 loop : -1.37 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1530 HIS 0.002 0.001 HIS A1483 PHE 0.021 0.001 PHE A 824 TYR 0.015 0.001 TYR A 649 ARG 0.006 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.120 Fit side-chains REVERT: A 514 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6590 (pp) REVERT: A 627 MET cc_start: 0.7340 (mtt) cc_final: 0.7001 (mtt) outliers start: 27 outliers final: 16 residues processed: 149 average time/residue: 0.2471 time to fit residues: 52.0186 Evaluate side-chains 140 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 973 ASN Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10889 Z= 0.202 Angle : 0.575 12.900 15036 Z= 0.285 Chirality : 0.041 0.327 1701 Planarity : 0.004 0.057 1726 Dihedral : 19.422 177.406 2200 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.56 % Allowed : 20.11 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.25), residues: 1217 helix: 0.45 (0.31), residues: 296 sheet: -0.86 (0.41), residues: 176 loop : -1.37 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1530 HIS 0.003 0.001 HIS A1483 PHE 0.024 0.001 PHE A 824 TYR 0.014 0.001 TYR A 649 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.075 Fit side-chains REVERT: A 514 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6612 (pp) REVERT: A 627 MET cc_start: 0.7328 (mtt) cc_final: 0.7030 (mtt) REVERT: A 1016 LYS cc_start: 0.6384 (pptt) cc_final: 0.6170 (tptt) outliers start: 23 outliers final: 18 residues processed: 147 average time/residue: 0.2292 time to fit residues: 47.5921 Evaluate side-chains 139 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 973 ASN Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 0.0050 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10889 Z= 0.205 Angle : 0.583 13.582 15036 Z= 0.288 Chirality : 0.041 0.328 1701 Planarity : 0.004 0.065 1726 Dihedral : 19.432 177.698 2200 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.33 % Allowed : 20.78 % Favored : 75.89 % 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 (0.25), residues: 1217 helix: 0.43 (0.31), residues: 296 sheet: -0.81 (0.41), residues: 176 loop : -1.37 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1530 HIS 0.007 0.001 HIS A 924 PHE 0.024 0.001 PHE A 824 TYR 0.017 0.002 TYR A 199 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.119 Fit side-chains REVERT: A 514 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6666 (pp) REVERT: A 564 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5699 (mtt180) REVERT: A 627 MET cc_start: 0.7386 (mtt) cc_final: 0.7086 (mtt) REVERT: A 1016 LYS cc_start: 0.6416 (pptt) cc_final: 0.6187 (tptt) outliers start: 30 outliers final: 21 residues processed: 141 average time/residue: 0.2236 time to fit residues: 44.4987 Evaluate side-chains 139 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 973 ASN Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 124 optimal weight: 0.0170 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10889 Z= 0.135 Angle : 0.563 13.659 15036 Z= 0.275 Chirality : 0.041 0.332 1701 Planarity : 0.004 0.060 1726 Dihedral : 19.293 176.885 2200 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.00 % Allowed : 21.44 % Favored : 75.56 % 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: -1.11 (0.25), residues: 1217 helix: 0.54 (0.31), residues: 296 sheet: -0.62 (0.42), residues: 171 loop : -1.34 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1530 HIS 0.005 0.001 HIS A1418 PHE 0.018 0.001 PHE A 824 TYR 0.018 0.001 TYR A 199 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.036 Fit side-chains REVERT: A 472 ARG cc_start: 0.6975 (tmm-80) cc_final: 0.6325 (ttp80) REVERT: A 514 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6407 (pp) REVERT: A 540 VAL cc_start: 0.6232 (t) cc_final: 0.5870 (p) REVERT: A 627 MET cc_start: 0.7390 (mtt) cc_final: 0.7078 (mtt) REVERT: A 1004 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7378 (tpt170) outliers start: 27 outliers final: 19 residues processed: 146 average time/residue: 0.2354 time to fit residues: 48.0943 Evaluate side-chains 142 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 973 ASN Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1536 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10889 Z= 0.195 Angle : 0.587 14.051 15036 Z= 0.288 Chirality : 0.041 0.319 1701 Planarity : 0.004 0.075 1726 Dihedral : 19.317 177.765 2200 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.78 % Allowed : 22.44 % Favored : 74.78 % 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: -1.14 (0.25), residues: 1217 helix: 0.52 (0.31), residues: 297 sheet: -0.56 (0.43), residues: 169 loop : -1.39 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1530 HIS 0.004 0.001 HIS A1418 PHE 0.024 0.001 PHE A 824 TYR 0.018 0.002 TYR A 199 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.127 Fit side-chains REVERT: A 472 ARG cc_start: 0.7014 (tmm-80) cc_final: 0.6680 (tmm160) REVERT: A 514 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6637 (pp) REVERT: A 922 TYR cc_start: 0.6132 (t80) cc_final: 0.5230 (t80) REVERT: A 1004 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7312 (tpt170) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 0.2397 time to fit residues: 48.1429 Evaluate side-chains 138 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 973 ASN Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10889 Z= 0.150 Angle : 0.583 14.128 15036 Z= 0.284 Chirality : 0.041 0.321 1701 Planarity : 0.004 0.063 1726 Dihedral : 19.260 177.205 2200 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.56 % Allowed : 23.11 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1217 helix: 0.51 (0.31), residues: 297 sheet: -0.60 (0.41), residues: 175 loop : -1.37 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1530 HIS 0.004 0.001 HIS A1418 PHE 0.021 0.001 PHE A 824 TYR 0.018 0.001 TYR A 199 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.108 Fit side-chains REVERT: A 472 ARG cc_start: 0.6984 (tmm-80) cc_final: 0.6366 (ttp80) REVERT: A 514 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6503 (pp) REVERT: A 540 VAL cc_start: 0.6272 (t) cc_final: 0.5961 (p) REVERT: A 922 TYR cc_start: 0.5895 (t80) cc_final: 0.5126 (t80) REVERT: A 1004 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7395 (tpt170) outliers start: 23 outliers final: 19 residues processed: 141 average time/residue: 0.2594 time to fit residues: 51.6854 Evaluate side-chains 143 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 973 ASN Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10889 Z= 0.173 Angle : 0.593 14.189 15036 Z= 0.288 Chirality : 0.041 0.320 1701 Planarity : 0.004 0.065 1726 Dihedral : 19.263 177.613 2200 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.67 % Allowed : 23.11 % Favored : 74.22 % 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: -1.14 (0.25), residues: 1217 helix: 0.50 (0.31), residues: 297 sheet: -0.49 (0.43), residues: 169 loop : -1.40 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1530 HIS 0.003 0.001 HIS A1418 PHE 0.022 0.001 PHE A 824 TYR 0.019 0.001 TYR A 199 ARG 0.004 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.091 Fit side-chains REVERT: A 472 ARG cc_start: 0.7053 (tmm-80) cc_final: 0.6744 (tmm160) REVERT: A 514 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6524 (pp) REVERT: A 627 MET cc_start: 0.7308 (mtt) cc_final: 0.7079 (mtt) REVERT: A 922 TYR cc_start: 0.5835 (t80) cc_final: 0.5155 (t80) REVERT: A 1004 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7326 (tpt170) outliers start: 24 outliers final: 19 residues processed: 137 average time/residue: 0.2318 time to fit residues: 44.9147 Evaluate side-chains 143 residues out of total 1078 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.0020 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 105 optimal weight: 0.0000 chunk 12 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.189823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.149991 restraints weight = 14772.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.156351 restraints weight = 7954.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.160485 restraints weight = 5366.928| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10889 Z= 0.129 Angle : 0.577 14.338 15036 Z= 0.279 Chirality : 0.041 0.325 1701 Planarity : 0.004 0.056 1726 Dihedral : 19.192 176.922 2200 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.22 % Allowed : 23.67 % Favored : 74.11 % 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: -1.12 (0.25), residues: 1217 helix: 0.57 (0.31), residues: 291 sheet: -0.52 (0.42), residues: 177 loop : -1.38 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1530 HIS 0.009 0.001 HIS A 924 PHE 0.019 0.001 PHE A 824 TYR 0.019 0.001 TYR A 199 ARG 0.004 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.90 seconds wall clock time: 40 minutes 16.92 seconds (2416.92 seconds total)