Starting phenix.real_space_refine on Mon Mar 11 06:25:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2g_30956/03_2024/7e2g_30956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2g_30956/03_2024/7e2g_30956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2g_30956/03_2024/7e2g_30956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2g_30956/03_2024/7e2g_30956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2g_30956/03_2024/7e2g_30956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e2g_30956/03_2024/7e2g_30956.pdb" } resolution = 3.61 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 4894 2.51 5 N 1114 2.21 5 O 1309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D ARG 631": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 703": "NH1" <-> "NH2" Residue "D GLU 751": "OE1" <-> "OE2" Residue "D GLU 775": "OE1" <-> "OE2" Residue "D PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 892": "NH1" <-> "NH2" Residue "D GLU 938": "OE1" <-> "OE2" Residue "D ARG 1078": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7376 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7376 Unusual residues: {'NAG': 4, 'Y01': 11} Classifications: {'peptide': 901, 'undetermined': 15} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 36, 'TRANS': 864, None: 15} Not linked: pdbres="PRO D1144 " pdbres="Y01 D1601 " Not linked: pdbres="Y01 D1601 " pdbres="Y01 D1602 " Not linked: pdbres="Y01 D1602 " pdbres="Y01 D1603 " Not linked: pdbres="Y01 D1603 " pdbres="Y01 D1604 " Not linked: pdbres="Y01 D1604 " pdbres="Y01 D1605 " ... (remaining 10 not shown) Chain breaks: 4 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 156 Time building chain proxies: 4.59, per 1000 atoms: 0.62 Number of scatterers: 7376 At special positions: 0 Unit cell: (104.76, 118.8, 114.48, 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 59 16.00 O 1309 8.00 N 1114 7.00 C 4894 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 Links applied NAG-ASN " NAG D1612 " - " ASN D 836 " " NAG D1613 " - " ASN D 476 " " NAG D1614 " - " ASN D 363 " " NAG D1615 " - " ASN D 917 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 58.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'D' and resid 181 through 186 removed outlier: 3.829A pdb=" N ILE D 185 " --> pdb=" O TYR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 210 removed outlier: 4.044A pdb=" N VAL D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 315 through 330 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.913A pdb=" N TYR D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 4.079A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 422 through 430 Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.932A pdb=" N TYR D 468 " --> pdb=" O MET D 464 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 470 " --> pdb=" O ASN D 466 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE D 472 " --> pdb=" O TYR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.616A pdb=" N TYR D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.778A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 548 Processing helix chain 'D' and resid 557 through 560 Processing helix chain 'D' and resid 561 through 587 removed outlier: 3.803A pdb=" N ILE D 565 " --> pdb=" O THR D 561 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN D 572 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA D 574 " --> pdb=" O GLY D 570 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 621 removed outlier: 5.077A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER D 607 " --> pdb=" O HIS D 603 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 627 through 659 removed outlier: 3.671A pdb=" N ARG D 631 " --> pdb=" O ILE D 627 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU D 652 " --> pdb=" O MET D 648 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 688 through 708 Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.600A pdb=" N CYS D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 738 removed outlier: 3.515A pdb=" N PHE D 723 " --> pdb=" O TYR D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 752 removed outlier: 3.858A pdb=" N PHE D 752 " --> pdb=" O LEU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 772 removed outlier: 3.684A pdb=" N ASP D 765 " --> pdb=" O PHE D 761 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS D 769 " --> pdb=" O ASP D 765 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 777 Processing helix chain 'D' and resid 820 through 835 Processing helix chain 'D' and resid 851 through 859 removed outlier: 3.989A pdb=" N THR D 855 " --> pdb=" O CYS D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 885 through 901 removed outlier: 4.211A pdb=" N LYS D 891 " --> pdb=" O GLU D 887 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 894 " --> pdb=" O ILE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 953 removed outlier: 4.308A pdb=" N SER D 953 " --> pdb=" O SER D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1004 removed outlier: 3.873A pdb=" N THR D1003 " --> pdb=" O MET D 999 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP D1004 " --> pdb=" O LEU D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1031 removed outlier: 3.669A pdb=" N TYR D1011 " --> pdb=" O ILE D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1050 removed outlier: 4.014A pdb=" N SER D1043 " --> pdb=" O SER D1039 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL D1046 " --> pdb=" O ILE D1042 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D1047 " --> pdb=" O SER D1043 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D1050 " --> pdb=" O VAL D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1059 removed outlier: 3.853A pdb=" N HIS D1055 " --> pdb=" O ASN D1051 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D1056 " --> pdb=" O PHE D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1072 through 1096 removed outlier: 5.665A pdb=" N SER D1081 " --> pdb=" O SER D1077 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA D1082 " --> pdb=" O ARG D1078 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D1090 " --> pdb=" O ALA D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 removed outlier: 3.717A pdb=" N THR D1106 " --> pdb=" O VAL D1102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 452 through 459 removed outlier: 4.133A pdb=" N SER D 301 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY D 486 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 306 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE D 484 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 789 through 790 Processing sheet with id=AA3, first strand: chain 'D' and resid 913 through 914 362 hydrogen bonds defined for protein. 1071 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: 2.01 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1120 1.32 - 1.44: 2064 1.44 - 1.56: 4310 1.56 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 7587 Sorted by residual: bond pdb=" C1 NAG D1612 " pdb=" O5 NAG D1612 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" CG ASN D 363 " pdb=" ND2 ASN D 363 " ideal model delta sigma weight residual 1.328 1.375 -0.047 2.10e-02 2.27e+03 5.08e+00 bond pdb=" C1 NAG D1614 " pdb=" O5 NAG D1614 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C ASN D 739 " pdb=" N PRO D 740 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.75e+00 bond pdb=" CG ASN D 917 " pdb=" ND2 ASN D 917 " ideal model delta sigma weight residual 1.328 1.365 -0.037 2.10e-02 2.27e+03 3.05e+00 ... (remaining 7582 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.66: 195 105.66 - 112.76: 4178 112.76 - 119.87: 2505 119.87 - 126.97: 3422 126.97 - 134.08: 96 Bond angle restraints: 10396 Sorted by residual: angle pdb=" N LYS D 805 " pdb=" CA LYS D 805 " pdb=" C LYS D 805 " ideal model delta sigma weight residual 113.19 108.39 4.80 1.19e+00 7.06e-01 1.62e+01 angle pdb=" C ASP D 906 " pdb=" N SER D 907 " pdb=" CA SER D 907 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ALA D 186 " pdb=" N ASP D 187 " pdb=" CA ASP D 187 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C THR D 228 " pdb=" N ALA D 229 " pdb=" CA ALA D 229 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C MET D 437 " pdb=" N THR D 438 " pdb=" CA THR D 438 " ideal model delta sigma weight residual 122.28 118.89 3.39 1.02e+00 9.61e-01 1.10e+01 ... (remaining 10391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 4703 22.08 - 44.16: 271 44.16 - 66.24: 40 66.24 - 88.32: 3 88.32 - 110.40: 4 Dihedral angle restraints: 5021 sinusoidal: 2372 harmonic: 2649 Sorted by residual: dihedral pdb=" CA ASN D 739 " pdb=" C ASN D 739 " pdb=" N PRO D 740 " pdb=" CA PRO D 740 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LYS D 256 " pdb=" C LYS D 256 " pdb=" N TYR D 257 " pdb=" CA TYR D 257 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP D 918 " pdb=" C ASP D 918 " pdb=" N THR D 919 " pdb=" CA THR D 919 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 1230 0.241 - 0.482: 0 0.482 - 0.723: 3 0.723 - 0.964: 0 0.964 - 1.205: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" C1 NAG D1615 " pdb=" ND2 ASN D 917 " pdb=" C2 NAG D1615 " pdb=" O5 NAG D1615 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" C1 NAG D1614 " pdb=" ND2 ASN D 363 " pdb=" C2 NAG D1614 " pdb=" O5 NAG D1614 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 NAG D1613 " pdb=" ND2 ASN D 476 " pdb=" C2 NAG D1613 " pdb=" O5 NAG D1613 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 1231 not shown) Planarity restraints: 1235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 557 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C PHE D 557 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE D 557 " -0.015 2.00e-02 2.50e+03 pdb=" N MET D 558 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 739 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO D 740 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 740 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 740 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 883 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLN D 883 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN D 883 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 884 " 0.013 2.00e-02 2.50e+03 ... (remaining 1232 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 136 2.69 - 3.24: 7644 3.24 - 3.79: 10657 3.79 - 4.35: 13430 4.35 - 4.90: 22539 Nonbonded interactions: 54406 Sorted by model distance: nonbonded pdb=" CAI Y01 D1610 " pdb=" CAR Y01 D1611 " model vdw 2.132 3.740 nonbonded pdb=" OH TYR D 357 " pdb=" OE1 GLN D 426 " model vdw 2.165 2.440 nonbonded pdb=" CAK Y01 D1610 " pdb=" CAT Y01 D1611 " model vdw 2.196 3.840 nonbonded pdb=" O ASP D 948 " pdb=" OG SER D 952 " model vdw 2.218 2.440 nonbonded pdb=" NZ LYS D 741 " pdb=" OAG Y01 D1607 " model vdw 2.236 2.520 ... (remaining 54401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.390 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: 1.760 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.760 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.005 0.094 7587 Z= 0.294 Angle : 0.717 7.525 10396 Z= 0.382 Chirality : 0.063 1.205 1234 Planarity : 0.004 0.058 1231 Dihedral : 13.567 110.396 3303 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.14 % Allowed : 5.99 % Favored : 93.88 % 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: -2.91 (0.25), residues: 891 helix: -0.61 (0.23), residues: 474 sheet: -2.20 (0.87), residues: 24 loop : -3.71 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 651 HIS 0.002 0.001 HIS D 551 PHE 0.020 0.001 PHE D 552 TYR 0.009 0.001 TYR D 636 ARG 0.003 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.820 Fit side-chains REVERT: D 431 LEU cc_start: 0.8989 (mp) cc_final: 0.8777 (mp) REVERT: D 595 GLU cc_start: 0.8169 (pt0) cc_final: 0.7954 (pt0) REVERT: D 700 GLU cc_start: 0.7949 (pt0) cc_final: 0.7439 (pt0) REVERT: D 738 ILE cc_start: 0.8156 (mm) cc_final: 0.7946 (mt) REVERT: D 926 GLU cc_start: 0.7668 (pp20) cc_final: 0.7266 (pp20) REVERT: D 960 GLU cc_start: 0.8744 (pp20) cc_final: 0.8291 (pp20) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.1385 time to fit residues: 27.3986 Evaluate side-chains 102 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 557 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN D 356 ASN D 422 ASN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN D 644 ASN ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 HIS ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7587 Z= 0.175 Angle : 0.647 10.976 10396 Z= 0.314 Chirality : 0.042 0.334 1234 Planarity : 0.004 0.048 1231 Dihedral : 9.649 72.025 1823 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.45 % Allowed : 11.97 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.28), residues: 891 helix: 0.91 (0.24), residues: 474 sheet: -1.49 (0.93), residues: 24 loop : -3.24 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 651 HIS 0.002 0.001 HIS D1055 PHE 0.021 0.001 PHE D 856 TYR 0.016 0.001 TYR D 430 ARG 0.002 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.887 Fit side-chains REVERT: D 205 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8098 (mp) REVERT: D 437 MET cc_start: 0.3637 (mmt) cc_final: 0.3410 (tpp) REVERT: D 700 GLU cc_start: 0.7905 (pt0) cc_final: 0.7472 (pt0) REVERT: D 739 ASN cc_start: 0.6888 (t0) cc_final: 0.6647 (t0) REVERT: D 768 TYR cc_start: 0.9053 (m-10) cc_final: 0.8688 (m-10) REVERT: D 877 TRP cc_start: 0.8697 (m100) cc_final: 0.8342 (m100) REVERT: D 920 ILE cc_start: 0.9282 (mp) cc_final: 0.9078 (tp) REVERT: D 960 GLU cc_start: 0.8444 (pp20) cc_final: 0.7486 (pp20) outliers start: 18 outliers final: 8 residues processed: 123 average time/residue: 0.1375 time to fit residues: 25.0486 Evaluate side-chains 108 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 1020 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.0000 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7587 Z= 0.238 Angle : 0.638 10.062 10396 Z= 0.312 Chirality : 0.041 0.331 1234 Planarity : 0.004 0.034 1231 Dihedral : 8.959 56.843 1823 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.72 % Allowed : 14.15 % Favored : 83.13 % 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: -0.64 (0.29), residues: 891 helix: 1.54 (0.24), residues: 474 sheet: -1.16 (0.96), residues: 24 loop : -3.08 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 651 HIS 0.003 0.001 HIS D 551 PHE 0.023 0.001 PHE D 856 TYR 0.010 0.001 TYR D 546 ARG 0.003 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.796 Fit side-chains REVERT: D 205 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8032 (mp) REVERT: D 453 MET cc_start: 0.9157 (ttm) cc_final: 0.8873 (ttt) REVERT: D 700 GLU cc_start: 0.7937 (pt0) cc_final: 0.7433 (pt0) REVERT: D 768 TYR cc_start: 0.9037 (m-10) cc_final: 0.8630 (m-10) REVERT: D 920 ILE cc_start: 0.9267 (mp) cc_final: 0.9057 (tp) REVERT: D 960 GLU cc_start: 0.8373 (pp20) cc_final: 0.7570 (pp20) outliers start: 20 outliers final: 12 residues processed: 118 average time/residue: 0.1386 time to fit residues: 24.3000 Evaluate side-chains 116 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7587 Z= 0.176 Angle : 0.602 12.748 10396 Z= 0.293 Chirality : 0.040 0.301 1234 Planarity : 0.003 0.033 1231 Dihedral : 8.829 59.226 1823 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.13 % Allowed : 14.83 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 891 helix: 1.82 (0.24), residues: 474 sheet: -0.98 (0.96), residues: 24 loop : -3.01 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 651 HIS 0.002 0.000 HIS D 551 PHE 0.024 0.001 PHE D 856 TYR 0.007 0.001 TYR D 645 ARG 0.003 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.878 Fit side-chains REVERT: D 205 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8053 (mp) REVERT: D 700 GLU cc_start: 0.7956 (pt0) cc_final: 0.7459 (pt0) REVERT: D 768 TYR cc_start: 0.8947 (m-10) cc_final: 0.8602 (m-10) REVERT: D 960 GLU cc_start: 0.8308 (pp20) cc_final: 0.7559 (pp20) outliers start: 23 outliers final: 15 residues processed: 122 average time/residue: 0.1425 time to fit residues: 25.9288 Evaluate side-chains 124 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 966 TRP Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7587 Z= 0.260 Angle : 0.626 11.388 10396 Z= 0.307 Chirality : 0.042 0.348 1234 Planarity : 0.004 0.034 1231 Dihedral : 8.893 57.954 1823 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.49 % Allowed : 15.65 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 891 helix: 1.86 (0.24), residues: 474 sheet: -0.98 (0.96), residues: 24 loop : -2.98 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 651 HIS 0.003 0.001 HIS D 829 PHE 0.024 0.001 PHE D 856 TYR 0.012 0.001 TYR D 546 ARG 0.003 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 0.818 Fit side-chains REVERT: D 205 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8106 (mp) REVERT: D 349 CYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7481 (m) REVERT: D 401 MET cc_start: 0.7081 (tmm) cc_final: 0.6863 (tmm) REVERT: D 453 MET cc_start: 0.9151 (ttm) cc_final: 0.8940 (ttt) REVERT: D 700 GLU cc_start: 0.7965 (pt0) cc_final: 0.7467 (pt0) REVERT: D 768 TYR cc_start: 0.9021 (m-80) cc_final: 0.8675 (m-10) REVERT: D 960 GLU cc_start: 0.8380 (pp20) cc_final: 0.7676 (pp20) outliers start: 33 outliers final: 21 residues processed: 124 average time/residue: 0.1293 time to fit residues: 24.5500 Evaluate side-chains 127 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1042 ILE Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.0040 chunk 17 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.0020 chunk 7 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7587 Z= 0.146 Angle : 0.586 13.247 10396 Z= 0.283 Chirality : 0.039 0.269 1234 Planarity : 0.003 0.032 1231 Dihedral : 8.695 57.996 1823 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.40 % Allowed : 16.73 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.29), residues: 891 helix: 2.02 (0.24), residues: 474 sheet: -0.82 (0.90), residues: 32 loop : -2.88 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 651 HIS 0.002 0.000 HIS D 941 PHE 0.024 0.001 PHE D 856 TYR 0.007 0.001 TYR D 257 ARG 0.003 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 0.825 Fit side-chains REVERT: D 205 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8038 (mp) REVERT: D 349 CYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7471 (m) REVERT: D 428 LEU cc_start: 0.9440 (mp) cc_final: 0.9067 (mp) REVERT: D 451 TYR cc_start: 0.8650 (m-80) cc_final: 0.8295 (m-80) REVERT: D 700 GLU cc_start: 0.7928 (pt0) cc_final: 0.7506 (pt0) REVERT: D 768 TYR cc_start: 0.8883 (m-80) cc_final: 0.8555 (m-10) REVERT: D 960 GLU cc_start: 0.8267 (pp20) cc_final: 0.7634 (pp20) REVERT: D 1036 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8437 (t) outliers start: 25 outliers final: 13 residues processed: 127 average time/residue: 0.1460 time to fit residues: 27.5473 Evaluate side-chains 124 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 966 TRP Chi-restraints excluded: chain D residue 1036 VAL Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7587 Z= 0.162 Angle : 0.583 13.403 10396 Z= 0.281 Chirality : 0.039 0.265 1234 Planarity : 0.003 0.033 1231 Dihedral : 8.612 59.133 1823 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.59 % Allowed : 17.96 % Favored : 79.46 % 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: 0.00 (0.29), residues: 891 helix: 2.09 (0.24), residues: 474 sheet: -0.73 (0.99), residues: 24 loop : -2.81 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 651 HIS 0.001 0.000 HIS D 941 PHE 0.022 0.001 PHE D 856 TYR 0.007 0.001 TYR D 546 ARG 0.003 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.711 Fit side-chains REVERT: D 205 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8042 (mp) REVERT: D 349 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (m) REVERT: D 428 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8974 (mp) REVERT: D 437 MET cc_start: 0.3558 (tpp) cc_final: 0.2610 (tpp) REVERT: D 451 TYR cc_start: 0.8624 (m-80) cc_final: 0.8233 (m-80) REVERT: D 700 GLU cc_start: 0.7952 (pt0) cc_final: 0.7651 (pt0) REVERT: D 723 PHE cc_start: 0.7911 (t80) cc_final: 0.7384 (t80) REVERT: D 768 TYR cc_start: 0.8898 (m-80) cc_final: 0.8530 (m-10) REVERT: D 960 GLU cc_start: 0.8260 (pp20) cc_final: 0.7607 (pp20) outliers start: 19 outliers final: 10 residues processed: 120 average time/residue: 0.1426 time to fit residues: 25.3781 Evaluate side-chains 118 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN D 356 ASN D 497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7587 Z= 0.231 Angle : 0.618 13.466 10396 Z= 0.300 Chirality : 0.040 0.264 1234 Planarity : 0.004 0.048 1231 Dihedral : 8.640 58.955 1823 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.27 % Allowed : 17.96 % Favored : 78.78 % 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: 0.01 (0.29), residues: 891 helix: 2.07 (0.24), residues: 475 sheet: -0.74 (0.97), residues: 24 loop : -2.79 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 651 HIS 0.002 0.000 HIS D 551 PHE 0.021 0.001 PHE D 856 TYR 0.012 0.001 TYR D 546 ARG 0.003 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.768 Fit side-chains REVERT: D 205 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8110 (mp) REVERT: D 349 CYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7500 (m) REVERT: D 352 TRP cc_start: 0.8668 (OUTLIER) cc_final: 0.8141 (t-100) REVERT: D 451 TYR cc_start: 0.8722 (m-80) cc_final: 0.8290 (m-80) REVERT: D 700 GLU cc_start: 0.7973 (pt0) cc_final: 0.7520 (pt0) REVERT: D 723 PHE cc_start: 0.7994 (t80) cc_final: 0.7447 (t80) REVERT: D 768 TYR cc_start: 0.8970 (m-80) cc_final: 0.8578 (m-10) REVERT: D 920 ILE cc_start: 0.9120 (mm) cc_final: 0.8870 (tp) REVERT: D 960 GLU cc_start: 0.8358 (pp20) cc_final: 0.7727 (pp20) REVERT: D 1116 MET cc_start: 0.8387 (tpp) cc_final: 0.7863 (mmt) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.1342 time to fit residues: 24.8687 Evaluate side-chains 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 352 TRP Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN D 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7587 Z= 0.176 Angle : 0.610 14.096 10396 Z= 0.292 Chirality : 0.039 0.260 1234 Planarity : 0.004 0.040 1231 Dihedral : 8.603 58.493 1823 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.45 % Allowed : 18.78 % Favored : 78.78 % 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: 0.07 (0.29), residues: 891 helix: 2.12 (0.24), residues: 474 sheet: -0.55 (1.02), residues: 24 loop : -2.75 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 651 HIS 0.001 0.000 HIS D 941 PHE 0.020 0.001 PHE D 856 TYR 0.008 0.001 TYR D 546 ARG 0.003 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.809 Fit side-chains REVERT: D 205 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8097 (mp) REVERT: D 349 CYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7470 (m) REVERT: D 428 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9099 (mp) REVERT: D 700 GLU cc_start: 0.7947 (pt0) cc_final: 0.7503 (pt0) REVERT: D 723 PHE cc_start: 0.7887 (t80) cc_final: 0.7331 (t80) REVERT: D 960 GLU cc_start: 0.8302 (pp20) cc_final: 0.7687 (pp20) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.1404 time to fit residues: 25.1383 Evaluate side-chains 122 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 968 VAL Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 72 optimal weight: 0.0370 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7587 Z= 0.176 Angle : 0.620 14.331 10396 Z= 0.295 Chirality : 0.040 0.257 1234 Planarity : 0.004 0.035 1231 Dihedral : 8.569 58.643 1823 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.59 % Allowed : 18.64 % Favored : 78.78 % 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: 0.12 (0.29), residues: 891 helix: 2.13 (0.24), residues: 474 sheet: -0.35 (1.06), residues: 24 loop : -2.71 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 651 HIS 0.001 0.000 HIS D 941 PHE 0.019 0.001 PHE D 856 TYR 0.009 0.001 TYR D 546 ARG 0.004 0.000 ARG D 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.822 Fit side-chains REVERT: D 205 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8100 (mp) REVERT: D 349 CYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7511 (m) REVERT: D 352 TRP cc_start: 0.8686 (OUTLIER) cc_final: 0.8404 (t-100) REVERT: D 428 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9090 (mp) REVERT: D 700 GLU cc_start: 0.7941 (pt0) cc_final: 0.7632 (pt0) REVERT: D 723 PHE cc_start: 0.7895 (t80) cc_final: 0.7341 (t80) REVERT: D 768 TYR cc_start: 0.8924 (m-80) cc_final: 0.8686 (m-10) REVERT: D 960 GLU cc_start: 0.8288 (pp20) cc_final: 0.7682 (pp20) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 0.1416 time to fit residues: 24.3603 Evaluate side-chains 119 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 352 TRP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 803 ASN Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.0050 chunk 72 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107415 restraints weight = 12745.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109404 restraints weight = 6974.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110593 restraints weight = 5028.545| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7587 Z= 0.149 Angle : 0.619 14.949 10396 Z= 0.290 Chirality : 0.040 0.404 1234 Planarity : 0.004 0.034 1231 Dihedral : 8.441 59.479 1823 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.04 % Allowed : 19.73 % Favored : 78.23 % 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: 0.19 (0.30), residues: 891 helix: 2.18 (0.24), residues: 474 sheet: -0.12 (1.09), residues: 24 loop : -2.68 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 651 HIS 0.001 0.000 HIS D 941 PHE 0.019 0.001 PHE D 996 TYR 0.009 0.001 TYR D 451 ARG 0.004 0.000 ARG D 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1527.22 seconds wall clock time: 28 minutes 57.59 seconds (1737.59 seconds total)