Starting phenix.real_space_refine on Mon Mar 11 12:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/03_2024/7q2z_13786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/03_2024/7q2z_13786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/03_2024/7q2z_13786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/03_2024/7q2z_13786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/03_2024/7q2z_13786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/03_2024/7q2z_13786.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 32 5.16 5 C 5130 2.51 5 N 1403 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 310": "OD1" <-> "OD2" Residue "E ASP 414": "OD1" <-> "OD2" Residue "E ASP 493": "OD1" <-> "OD2" Residue "E TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 676": "OD1" <-> "OD2" 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: 8258 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 6543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6543 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 19, 'TRANS': 792} Chain breaks: 4 Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 772 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 460 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "G" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 483 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Time building chain proxies: 4.72, per 1000 atoms: 0.57 Number of scatterers: 8258 At special positions: 0 Unit cell: (85.32, 109.08, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 46 15.00 O 1647 8.00 N 1403 7.00 C 5130 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: 3.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1754 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 77.3% alpha, 0.0% beta 19 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'E' and resid 8 through 25 Processing helix chain 'E' and resid 32 through 49 Processing helix chain 'E' and resid 50 through 64 removed outlier: 3.839A pdb=" N PHE E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 99 removed outlier: 3.547A pdb=" N ILE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 92 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 123 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 130 through 145 Processing helix chain 'E' and resid 152 through 167 Processing helix chain 'E' and resid 171 through 183 Processing helix chain 'E' and resid 206 through 217 removed outlier: 3.972A pdb=" N GLN E 215 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 229 removed outlier: 3.548A pdb=" N ARG E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 248 through 258 removed outlier: 3.645A pdb=" N VAL E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 288 through 301 removed outlier: 3.589A pdb=" N ARG E 292 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 311 through 318 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.994A pdb=" N GLU E 331 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 355 through 372 removed outlier: 3.577A pdb=" N ASN E 372 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 381 removed outlier: 3.607A pdb=" N LEU E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.563A pdb=" N GLU E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR E 395 " --> pdb=" O HIS E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 removed outlier: 4.090A pdb=" N ARG E 431 " --> pdb=" O ILE E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 452 removed outlier: 3.634A pdb=" N ARG E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 474 through 503 removed outlier: 4.091A pdb=" N PHE E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL E 479 " --> pdb=" O GLU E 475 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS E 502 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 587 removed outlier: 3.767A pdb=" N TYR E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 585 " --> pdb=" O ARG E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 606 removed outlier: 3.614A pdb=" N ALA E 600 " --> pdb=" O ASN E 596 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 604 " --> pdb=" O ALA E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 612 removed outlier: 4.052A pdb=" N ARG E 612 " --> pdb=" O THR E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 631 Processing helix chain 'E' and resid 633 through 640 removed outlier: 3.623A pdb=" N ALA E 637 " --> pdb=" O ASP E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 650 Processing helix chain 'E' and resid 652 through 670 Processing helix chain 'E' and resid 671 through 675 removed outlier: 3.991A pdb=" N VAL E 674 " --> pdb=" O GLY E 671 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 675 " --> pdb=" O ASN E 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 671 through 675' Processing helix chain 'E' and resid 682 through 696 removed outlier: 4.023A pdb=" N LEU E 686 " --> pdb=" O ASP E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 716 removed outlier: 3.527A pdb=" N ALA E 716 " --> pdb=" O LYS E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 733 removed outlier: 3.995A pdb=" N PHE E 725 " --> pdb=" O ASP E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 739 removed outlier: 3.613A pdb=" N SER E 738 " --> pdb=" O PRO E 735 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER E 739 " --> pdb=" O ILE E 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 735 through 739' Processing helix chain 'E' and resid 740 through 758 removed outlier: 3.576A pdb=" N VAL E 744 " --> pdb=" O ASN E 740 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE E 749 " --> pdb=" O GLN E 745 " (cutoff:3.500A) Proline residue: E 752 - end of helix removed outlier: 4.121A pdb=" N HIS E 758 " --> pdb=" O TYR E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 785 removed outlier: 3.736A pdb=" N THR E 768 " --> pdb=" O ARG E 764 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA E 770 " --> pdb=" O SER E 766 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASP E 771 " --> pdb=" O ARG E 767 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 778 " --> pdb=" O LEU E 774 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 779 " --> pdb=" O ARG E 775 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP E 781 " --> pdb=" O CYS E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 810 Processing helix chain 'E' and resid 811 through 815 removed outlier: 3.855A pdb=" N LEU E 815 " --> pdb=" O PRO E 812 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 824 removed outlier: 4.244A pdb=" N LYS E 823 " --> pdb=" O GLY E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 827 through 839 removed outlier: 3.738A pdb=" N PHE E 831 " --> pdb=" O VAL E 827 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 842 No H-bonds generated for 'chain 'E' and resid 840 through 842' Processing helix chain 'E' and resid 844 through 854 removed outlier: 3.901A pdb=" N LYS E 848 " --> pdb=" O LYS E 844 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN E 854 " --> pdb=" O MET E 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 882 Processing helix chain 'E' and resid 887 through 909 Processing helix chain 'C' and resid 388 through 398 Processing helix chain 'C' and resid 468 through 475 removed outlier: 4.004A pdb=" N ASP C 472 " --> pdb=" O ASP C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 removed outlier: 4.247A pdb=" N LYS C 491 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 511 430 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2310 1.34 - 1.45: 1458 1.45 - 1.57: 4579 1.57 - 1.69: 91 1.69 - 1.81: 50 Bond restraints: 8488 Sorted by residual: bond pdb=" CB PRO E 592 " pdb=" CG PRO E 592 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.83e+00 bond pdb=" O3' DA G 13 " pdb=" P DA G 14 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.50e-02 4.44e+03 2.21e+00 bond pdb=" C3' DT F 3 " pdb=" O3' DT F 3 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" O3' DT F 11 " pdb=" P DT F 12 " ideal model delta sigma weight residual 1.607 1.590 0.017 1.50e-02 4.44e+03 1.28e+00 bond pdb=" O3' DT F 12 " pdb=" P DT F 13 " ideal model delta sigma weight residual 1.607 1.590 0.017 1.50e-02 4.44e+03 1.27e+00 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 427 106.72 - 113.54: 4682 113.54 - 120.37: 3283 120.37 - 127.20: 3126 127.20 - 134.02: 139 Bond angle restraints: 11657 Sorted by residual: angle pdb=" C4' DA G 12 " pdb=" C3' DA G 12 " pdb=" O3' DA G 12 " ideal model delta sigma weight residual 110.00 105.30 4.70 1.50e+00 4.44e-01 9.82e+00 angle pdb=" C4' DT F 13 " pdb=" O4' DT F 13 " pdb=" C1' DT F 13 " ideal model delta sigma weight residual 109.70 105.97 3.73 1.50e+00 4.44e-01 6.18e+00 angle pdb=" C4' DT F 13 " pdb=" C3' DT F 13 " pdb=" O3' DT F 13 " ideal model delta sigma weight residual 110.00 106.27 3.73 1.50e+00 4.44e-01 6.18e+00 angle pdb=" CA PRO E 592 " pdb=" N PRO E 592 " pdb=" CD PRO E 592 " ideal model delta sigma weight residual 112.00 108.53 3.47 1.40e+00 5.10e-01 6.15e+00 angle pdb=" N GLU E 874 " pdb=" CA GLU E 874 " pdb=" CB GLU E 874 " ideal model delta sigma weight residual 110.28 114.09 -3.81 1.55e+00 4.16e-01 6.03e+00 ... (remaining 11652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 4817 34.83 - 69.66: 279 69.66 - 104.48: 11 104.48 - 139.31: 0 139.31 - 174.14: 1 Dihedral angle restraints: 5108 sinusoidal: 2435 harmonic: 2673 Sorted by residual: dihedral pdb=" C4' DT F 3 " pdb=" C3' DT F 3 " pdb=" O3' DT F 3 " pdb=" P DT F 4 " ideal model delta sinusoidal sigma weight residual 220.00 45.86 174.14 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP E 302 " pdb=" CB ASP E 302 " pdb=" CG ASP E 302 " pdb=" OD1 ASP E 302 " ideal model delta sinusoidal sigma weight residual -30.00 -86.83 56.83 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP E 286 " pdb=" CB ASP E 286 " pdb=" CG ASP E 286 " pdb=" OD1 ASP E 286 " ideal model delta sinusoidal sigma weight residual -30.00 -82.99 52.99 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 5105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 987 0.034 - 0.067: 292 0.067 - 0.101: 61 0.101 - 0.135: 7 0.135 - 0.168: 1 Chirality restraints: 1348 Sorted by residual: chirality pdb=" C3' DA G 12 " pdb=" C4' DA G 12 " pdb=" O3' DA G 12 " pdb=" C2' DA G 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA PRO E 799 " pdb=" N PRO E 799 " pdb=" C PRO E 799 " pdb=" CB PRO E 799 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" C4' DT F 13 " pdb=" C5' DT F 13 " pdb=" O4' DT F 13 " pdb=" C3' DT F 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.41 -0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 1345 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 591 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO E 592 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 592 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 592 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 272 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO E 273 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 273 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 273 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA G 13 " -0.022 2.00e-02 2.50e+03 1.03e-02 2.91e+00 pdb=" N9 DA G 13 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA G 13 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA G 13 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA G 13 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA G 13 " -0.009 2.00e-02 2.50e+03 pdb=" N6 DA G 13 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA G 13 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA G 13 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA G 13 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA G 13 " 0.007 2.00e-02 2.50e+03 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1291 2.76 - 3.30: 7672 3.30 - 3.83: 13540 3.83 - 4.37: 15544 4.37 - 4.90: 26188 Nonbonded interactions: 64235 Sorted by model distance: nonbonded pdb=" O SER E 601 " pdb=" OG1 THR E 605 " model vdw 2.227 2.440 nonbonded pdb=" O PRO E 383 " pdb=" OH TYR E 432 " model vdw 2.231 2.440 nonbonded pdb=" O ASP E 782 " pdb=" OG SER E 786 " model vdw 2.251 2.440 nonbonded pdb=" O ASP E 319 " pdb=" N SER E 321 " model vdw 2.283 2.520 nonbonded pdb=" OE1 GLN E 22 " pdb=" NE2 GLN E 25 " model vdw 2.306 2.520 ... (remaining 64230 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 individual isotropic 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.440 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.660 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 0.084 8488 Z= 0.159 Angle : 0.483 5.347 11657 Z= 0.282 Chirality : 0.033 0.168 1348 Planarity : 0.004 0.083 1325 Dihedral : 18.984 174.140 3354 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.53 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.44 (0.26), residues: 888 helix: -0.12 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.95 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 57 HIS 0.003 0.001 HIS E 394 PHE 0.009 0.001 PHE E 360 TYR 0.009 0.001 TYR E 168 ARG 0.004 0.000 ARG E 775 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.919 Fit side-chains REVERT: E 23 LYS cc_start: 0.7039 (ttmm) cc_final: 0.6707 (mptt) REVERT: E 69 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7530 (tttm) REVERT: E 312 ILE cc_start: 0.8625 (mm) cc_final: 0.8179 (mm) REVERT: E 434 TYR cc_start: 0.8136 (m-80) cc_final: 0.7042 (m-10) REVERT: E 466 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7048 (mmm-85) REVERT: E 488 ASP cc_start: 0.6882 (m-30) cc_final: 0.6598 (m-30) REVERT: E 496 LYS cc_start: 0.7749 (tttm) cc_final: 0.7548 (tttt) REVERT: E 697 ASN cc_start: 0.7293 (t0) cc_final: 0.7077 (t0) REVERT: E 838 ILE cc_start: 0.8424 (mt) cc_final: 0.8172 (pt) REVERT: C 482 LYS cc_start: 0.7247 (mtmm) cc_final: 0.6785 (pttp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2829 time to fit residues: 64.6869 Evaluate side-chains 99 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 381 ASN E 391 HIS C 489 ASN C 492 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8488 Z= 0.193 Angle : 0.506 7.088 11657 Z= 0.275 Chirality : 0.036 0.113 1348 Planarity : 0.004 0.060 1325 Dihedral : 19.668 175.426 1516 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 1.22 % Allowed : 7.65 % Favored : 91.13 % 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: 0.19 (0.29), residues: 888 helix: 1.09 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -2.45 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 408 HIS 0.003 0.001 HIS E 274 PHE 0.016 0.001 PHE E 733 TYR 0.010 0.001 TYR E 657 ARG 0.005 0.001 ARG E 793 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.909 Fit side-chains REVERT: E 23 LYS cc_start: 0.6655 (ttmm) cc_final: 0.6302 (mptt) REVERT: E 170 ARG cc_start: 0.7460 (ttm170) cc_final: 0.6865 (ttm170) REVERT: E 297 ARG cc_start: 0.8070 (tpt170) cc_final: 0.7784 (ttm-80) REVERT: E 312 ILE cc_start: 0.8924 (mm) cc_final: 0.8668 (mm) REVERT: E 344 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7226 (mt) REVERT: E 466 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7218 (mmm-85) REVERT: E 496 LYS cc_start: 0.7749 (tttm) cc_final: 0.7535 (tttt) REVERT: E 604 ASP cc_start: 0.8235 (p0) cc_final: 0.7987 (p0) REVERT: E 641 MET cc_start: 0.8685 (mmt) cc_final: 0.8076 (mmt) REVERT: E 646 MET cc_start: 0.7077 (mmm) cc_final: 0.6766 (mmp) REVERT: E 688 LYS cc_start: 0.7431 (mtmt) cc_final: 0.7098 (mmtm) REVERT: E 823 LYS cc_start: 0.8091 (ptmt) cc_final: 0.7873 (ptmt) REVERT: C 397 ASN cc_start: 0.8003 (m110) cc_final: 0.7666 (m-40) REVERT: C 482 LYS cc_start: 0.7410 (mtmm) cc_final: 0.6964 (ptpt) REVERT: C 510 THR cc_start: 0.8744 (m) cc_final: 0.8425 (m) outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 0.2550 time to fit residues: 37.4472 Evaluate side-chains 102 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 888 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN E 335 GLN E 737 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8488 Z= 0.249 Angle : 0.533 7.730 11657 Z= 0.288 Chirality : 0.037 0.133 1348 Planarity : 0.004 0.051 1325 Dihedral : 19.569 177.009 1516 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 1.70 % Allowed : 9.23 % Favored : 89.06 % 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: 0.65 (0.29), residues: 888 helix: 1.44 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.31 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 780 HIS 0.004 0.001 HIS E 274 PHE 0.018 0.002 PHE E 382 TYR 0.012 0.001 TYR E 366 ARG 0.004 0.001 ARG E 793 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.928 Fit side-chains REVERT: E 23 LYS cc_start: 0.6981 (ttmm) cc_final: 0.6579 (mptt) REVERT: E 170 ARG cc_start: 0.7614 (ttm170) cc_final: 0.7101 (ttm170) REVERT: E 297 ARG cc_start: 0.8135 (tpt170) cc_final: 0.7816 (ttm-80) REVERT: E 322 ARG cc_start: 0.7878 (ptm160) cc_final: 0.7440 (ptp-170) REVERT: E 344 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7421 (mt) REVERT: E 466 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7193 (mtm-85) REVERT: E 496 LYS cc_start: 0.7815 (tttm) cc_final: 0.7491 (tttt) REVERT: E 603 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7735 (mtp) REVERT: E 688 LYS cc_start: 0.7388 (mtmt) cc_final: 0.7043 (mmtm) REVERT: E 823 LYS cc_start: 0.8091 (ptmt) cc_final: 0.7829 (ptmt) REVERT: E 879 ILE cc_start: 0.7865 (mm) cc_final: 0.7597 (mm) REVERT: C 397 ASN cc_start: 0.8056 (m110) cc_final: 0.7845 (m-40) REVERT: C 482 LYS cc_start: 0.7525 (mtmm) cc_final: 0.6997 (ptpt) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.2366 time to fit residues: 33.8711 Evaluate side-chains 103 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 603 MET Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 838 ILE Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 737 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8488 Z= 0.156 Angle : 0.462 6.383 11657 Z= 0.254 Chirality : 0.034 0.114 1348 Planarity : 0.003 0.048 1325 Dihedral : 19.401 176.760 1516 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 1.46 % Allowed : 10.33 % Favored : 88.21 % 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 (0.29), residues: 888 helix: 1.84 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 780 HIS 0.003 0.001 HIS E 394 PHE 0.012 0.001 PHE E 733 TYR 0.012 0.001 TYR E 657 ARG 0.003 0.000 ARG E 793 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.907 Fit side-chains REVERT: E 23 LYS cc_start: 0.6840 (ttmm) cc_final: 0.6440 (mptt) REVERT: E 170 ARG cc_start: 0.7573 (ttm170) cc_final: 0.7051 (ttm170) REVERT: E 297 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7802 (ttm-80) REVERT: E 322 ARG cc_start: 0.7841 (ptm160) cc_final: 0.7389 (ptp-170) REVERT: E 344 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7199 (mt) REVERT: E 466 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7201 (mtm-85) REVERT: E 496 LYS cc_start: 0.7829 (tttm) cc_final: 0.7521 (tttt) REVERT: E 603 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7669 (mtp) REVERT: E 646 MET cc_start: 0.7153 (mmm) cc_final: 0.6930 (mmp) REVERT: E 688 LYS cc_start: 0.7234 (mtmt) cc_final: 0.6968 (mmtm) REVERT: E 879 ILE cc_start: 0.7784 (mm) cc_final: 0.7413 (mm) REVERT: C 397 ASN cc_start: 0.8029 (m110) cc_final: 0.7823 (m-40) REVERT: C 482 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7135 (ptpt) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.2448 time to fit residues: 33.4434 Evaluate side-chains 100 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 603 MET Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 838 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 GLN E 147 ASN E 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8488 Z= 0.148 Angle : 0.449 6.047 11657 Z= 0.248 Chirality : 0.034 0.113 1348 Planarity : 0.003 0.048 1325 Dihedral : 19.429 177.150 1516 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer: Outliers : 1.46 % Allowed : 11.18 % Favored : 87.36 % 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: 1.56 (0.30), residues: 888 helix: 2.03 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -1.71 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 780 HIS 0.002 0.001 HIS E 394 PHE 0.011 0.001 PHE E 733 TYR 0.012 0.001 TYR E 657 ARG 0.003 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.907 Fit side-chains REVERT: E 23 LYS cc_start: 0.6833 (ttmm) cc_final: 0.6424 (mptt) REVERT: E 170 ARG cc_start: 0.7559 (ttm170) cc_final: 0.7032 (ttm170) REVERT: E 297 ARG cc_start: 0.8106 (tpt170) cc_final: 0.7821 (ttm-80) REVERT: E 344 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7194 (mt) REVERT: E 466 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7250 (mtm-85) REVERT: E 496 LYS cc_start: 0.7792 (tttm) cc_final: 0.7463 (tttt) REVERT: E 641 MET cc_start: 0.8762 (tpp) cc_final: 0.8243 (mmt) REVERT: E 879 ILE cc_start: 0.7731 (mm) cc_final: 0.7366 (mm) REVERT: C 397 ASN cc_start: 0.7982 (m110) cc_final: 0.7773 (m-40) REVERT: C 482 LYS cc_start: 0.7649 (mtmm) cc_final: 0.7204 (ptpt) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.2378 time to fit residues: 32.4704 Evaluate side-chains 97 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 335 GLN E 737 ASN E 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8488 Z= 0.147 Angle : 0.446 6.147 11657 Z= 0.246 Chirality : 0.034 0.112 1348 Planarity : 0.003 0.047 1325 Dihedral : 19.396 177.250 1516 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.64 % Rotamer: Outliers : 1.46 % Allowed : 11.30 % Favored : 87.24 % 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: 1.77 (0.30), residues: 888 helix: 2.17 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.58 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 780 HIS 0.002 0.001 HIS E 394 PHE 0.010 0.001 PHE E 733 TYR 0.012 0.001 TYR E 657 ARG 0.003 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.887 Fit side-chains REVERT: E 23 LYS cc_start: 0.6824 (ttmm) cc_final: 0.6454 (mptt) REVERT: E 170 ARG cc_start: 0.7552 (ttm170) cc_final: 0.7018 (ttm170) REVERT: E 297 ARG cc_start: 0.8064 (tpt170) cc_final: 0.7787 (ttm-80) REVERT: E 344 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7232 (mt) REVERT: E 379 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: E 466 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7248 (mtm-85) REVERT: E 496 LYS cc_start: 0.7825 (tttm) cc_final: 0.7471 (tttt) REVERT: E 603 MET cc_start: 0.8005 (mtp) cc_final: 0.7725 (ttp) REVERT: E 879 ILE cc_start: 0.7731 (mm) cc_final: 0.7366 (mm) REVERT: C 482 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7238 (ptpt) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.2267 time to fit residues: 31.0242 Evaluate side-chains 100 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8488 Z= 0.126 Angle : 0.427 6.942 11657 Z= 0.236 Chirality : 0.033 0.107 1348 Planarity : 0.003 0.046 1325 Dihedral : 19.325 177.041 1516 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.91 % Favored : 97.97 % Rotamer: Outliers : 1.34 % Allowed : 11.42 % Favored : 87.24 % 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: 2.04 (0.30), residues: 888 helix: 2.34 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.44 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 780 HIS 0.002 0.000 HIS E 394 PHE 0.007 0.001 PHE E 382 TYR 0.011 0.001 TYR E 657 ARG 0.003 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.903 Fit side-chains REVERT: E 23 LYS cc_start: 0.6768 (ttmm) cc_final: 0.6375 (mptt) REVERT: E 44 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7413 (mmtm) REVERT: E 170 ARG cc_start: 0.7499 (ttm170) cc_final: 0.6959 (ttm170) REVERT: E 297 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7768 (ttm-80) REVERT: E 344 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7164 (mt) REVERT: E 379 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: E 458 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6944 (mt-10) REVERT: E 466 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7252 (mtm-85) REVERT: E 496 LYS cc_start: 0.7826 (tttm) cc_final: 0.7467 (tttt) REVERT: E 691 TYR cc_start: 0.8412 (m-80) cc_final: 0.8149 (m-80) REVERT: E 879 ILE cc_start: 0.7622 (mm) cc_final: 0.7290 (mm) REVERT: C 482 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7367 (ptpp) outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 0.2339 time to fit residues: 32.5560 Evaluate side-chains 98 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.0040 chunk 79 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 335 GLN E 381 ASN E 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8488 Z= 0.309 Angle : 0.562 7.552 11657 Z= 0.302 Chirality : 0.038 0.146 1348 Planarity : 0.004 0.047 1325 Dihedral : 19.580 177.570 1516 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 1.46 % Allowed : 11.30 % Favored : 87.24 % 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: 1.49 (0.29), residues: 888 helix: 1.87 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.48 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 351 HIS 0.004 0.001 HIS E 274 PHE 0.018 0.002 PHE E 733 TYR 0.014 0.002 TYR E 366 ARG 0.005 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.912 Fit side-chains REVERT: E 23 LYS cc_start: 0.7194 (ttmm) cc_final: 0.6755 (mptt) REVERT: E 44 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7521 (mmtm) REVERT: E 170 ARG cc_start: 0.7680 (ttm170) cc_final: 0.7146 (ttm170) REVERT: E 297 ARG cc_start: 0.8126 (tpt170) cc_final: 0.7777 (ttm-80) REVERT: E 322 ARG cc_start: 0.7886 (ptm160) cc_final: 0.7611 (ptp-170) REVERT: E 344 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7460 (mt) REVERT: E 379 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: E 466 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7222 (mtm-85) REVERT: E 496 LYS cc_start: 0.7836 (tttm) cc_final: 0.7443 (tttt) REVERT: C 482 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7312 (ptpt) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.2567 time to fit residues: 36.6036 Evaluate side-chains 99 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8488 Z= 0.163 Angle : 0.472 7.944 11657 Z= 0.258 Chirality : 0.034 0.120 1348 Planarity : 0.003 0.046 1325 Dihedral : 19.424 177.471 1516 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.14 % Favored : 97.75 % Rotamer: Outliers : 1.46 % Allowed : 11.79 % Favored : 86.76 % 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: 1.87 (0.30), residues: 888 helix: 2.18 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 780 HIS 0.004 0.001 HIS E 401 PHE 0.016 0.001 PHE C 523 TYR 0.013 0.001 TYR E 657 ARG 0.004 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.969 Fit side-chains REVERT: E 23 LYS cc_start: 0.6830 (ttmm) cc_final: 0.6468 (mptt) REVERT: E 44 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7517 (mmtm) REVERT: E 170 ARG cc_start: 0.7640 (ttm170) cc_final: 0.7115 (ttm170) REVERT: E 297 ARG cc_start: 0.8081 (tpt170) cc_final: 0.7761 (ttm-80) REVERT: E 344 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7373 (mt) REVERT: E 379 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: E 466 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7187 (mtm-85) REVERT: E 496 LYS cc_start: 0.7830 (tttm) cc_final: 0.7472 (tttt) REVERT: E 641 MET cc_start: 0.8621 (mmt) cc_final: 0.8055 (mmt) REVERT: E 879 ILE cc_start: 0.7791 (mm) cc_final: 0.7279 (mm) REVERT: C 482 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7395 (ptpt) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.2340 time to fit residues: 31.5073 Evaluate side-chains 97 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8488 Z= 0.159 Angle : 0.468 8.421 11657 Z= 0.255 Chirality : 0.034 0.120 1348 Planarity : 0.003 0.046 1325 Dihedral : 19.413 177.313 1516 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 1.46 % Allowed : 11.91 % Favored : 86.63 % 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: 2.03 (0.30), residues: 888 helix: 2.26 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 780 HIS 0.004 0.001 HIS E 401 PHE 0.016 0.001 PHE C 523 TYR 0.012 0.001 TYR E 657 ARG 0.004 0.000 ARG E 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.886 Fit side-chains REVERT: E 23 LYS cc_start: 0.6814 (ttmm) cc_final: 0.6438 (mptt) REVERT: E 44 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7547 (mmtm) REVERT: E 170 ARG cc_start: 0.7648 (ttm170) cc_final: 0.7094 (ttm170) REVERT: E 297 ARG cc_start: 0.8057 (tpt170) cc_final: 0.7767 (ttm-80) REVERT: E 344 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7356 (mt) REVERT: E 379 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: E 466 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7243 (mtm-85) REVERT: E 496 LYS cc_start: 0.7803 (tttm) cc_final: 0.7437 (tttt) REVERT: E 641 MET cc_start: 0.8645 (mmt) cc_final: 0.8138 (mmt) REVERT: E 877 ASP cc_start: 0.7363 (m-30) cc_final: 0.7064 (m-30) REVERT: E 879 ILE cc_start: 0.7762 (mm) cc_final: 0.7244 (mm) REVERT: C 482 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7402 (ptpt) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.2327 time to fit residues: 31.3930 Evaluate side-chains 102 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain C residue 509 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.162823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122457 restraints weight = 9146.671| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.30 r_work: 0.3096 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8488 Z= 0.128 Angle : 0.443 8.249 11657 Z= 0.243 Chirality : 0.033 0.121 1348 Planarity : 0.003 0.045 1325 Dihedral : 19.345 177.492 1516 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.03 % Favored : 97.86 % Rotamer: Outliers : 1.46 % Allowed : 11.91 % Favored : 86.63 % 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: 2.28 (0.30), residues: 888 helix: 2.46 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.17 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 780 HIS 0.003 0.000 HIS E 401 PHE 0.016 0.001 PHE C 523 TYR 0.012 0.001 TYR E 657 ARG 0.004 0.000 ARG E 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.96 seconds wall clock time: 33 minutes 20.34 seconds (2000.34 seconds total)