Starting phenix.real_space_refine (version: dev) on Sat Feb 18 13:47:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/02_2023/7q2z_13786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/02_2023/7q2z_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_13786/02_2023/7q2z_13786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/02_2023/7q2z_13786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/02_2023/7q2z_13786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2z_13786/02_2023/7q2z_13786.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.67, 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: 3.70 Conformation dependent library (CDL) restraints added in 1.1 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: 2.49 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: 3.20 Time building geometry restraints manager: 3.72 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: 4736 34.83 - 69.66: 268 69.66 - 104.48: 11 104.48 - 139.31: 0 139.31 - 174.14: 1 Dihedral angle restraints: 5016 sinusoidal: 2343 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 5013 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 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. 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: 0.150 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: 1.780 Check model and map are aligned: 0.120 Process input model: 26.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 18.780 174.140 3262 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 % 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 *********************** 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 : 0.944 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2853 time to fit residues: 64.9397 Evaluate side-chains 94 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2532 ------------------------------------------------------------------------------- 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: 7.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 147 ASN E 381 ASN E 391 HIS C 489 ASN C 492 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 8488 Z= 0.238 Angle : 0.544 7.290 11657 Z= 0.294 Chirality : 0.037 0.120 1348 Planarity : 0.004 0.060 1325 Dihedral : 19.578 175.777 1424 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer Outliers : 1.34 % 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: 0.06 (0.28), residues: 888 helix: 0.99 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 249 *********************** 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 110 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.879 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.2701 time to fit residues: 39.5941 Evaluate side-chains 94 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0911 time to fit residues: 2.7141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 335 GLN E 737 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 8488 Z= 0.297 Angle : 0.570 8.098 11657 Z= 0.306 Chirality : 0.038 0.141 1348 Planarity : 0.004 0.052 1325 Dihedral : 19.625 177.028 1424 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.95 % Rotamer Outliers : 0.73 % 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: 0.49 (0.28), residues: 888 helix: 1.30 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.29 (0.34), residues: 250 *********************** 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 96 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.928 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.2070 time to fit residues: 27.5655 Evaluate side-chains 82 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0947 time to fit residues: 1.9989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 0.0470 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 147 ASN E 335 GLN E 381 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3340 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= 0.236 Angle : 0.515 7.173 11657 Z= 0.279 Chirality : 0.036 0.129 1348 Planarity : 0.004 0.049 1325 Dihedral : 19.579 176.727 1424 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer Outliers : 0.36 % 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: 0.92 (0.29), residues: 888 helix: 1.58 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.98 (0.36), residues: 252 *********************** 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 93 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.900 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.2300 time to fit residues: 29.3549 Evaluate side-chains 85 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0778 time to fit residues: 1.5973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 335 GLN E 703 GLN E 737 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3292 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= 0.145 Angle : 0.453 6.003 11657 Z= 0.250 Chirality : 0.034 0.109 1348 Planarity : 0.003 0.048 1325 Dihedral : 19.449 176.784 1424 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 888 helix: 1.98 (0.21), residues: 635 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 253 *********************** 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 88 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.933 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2183 time to fit residues: 27.1610 Evaluate side-chains 80 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 E 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3329 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= 0.135 Angle : 0.438 5.896 11657 Z= 0.242 Chirality : 0.033 0.110 1348 Planarity : 0.003 0.049 1325 Dihedral : 19.372 176.847 1424 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.52 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 888 helix: 2.19 (0.21), residues: 637 sheet: None (None), residues: 0 loop : -1.60 (0.37), residues: 251 *********************** 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 100 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.970 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.2121 time to fit residues: 29.3913 Evaluate side-chains 88 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0830 time to fit residues: 1.9565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3391 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 : 0.456 6.780 11657 Z= 0.251 Chirality : 0.034 0.123 1348 Planarity : 0.003 0.050 1325 Dihedral : 19.391 176.822 1424 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer Outliers : 0.49 % 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: 1.85 (0.29), residues: 888 helix: 2.20 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 246 *********************** 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 93 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.006 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 91 average time/residue: 0.2164 time to fit residues: 27.9761 Evaluate side-chains 87 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0800 time to fit residues: 1.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 335 GLN E 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3435 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= 0.150 Angle : 0.454 7.389 11657 Z= 0.251 Chirality : 0.034 0.120 1348 Planarity : 0.003 0.048 1325 Dihedral : 19.356 176.862 1424 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer Outliers : 0.36 % 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: 2.01 (0.30), residues: 888 helix: 2.29 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.39 (0.39), residues: 245 *********************** 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 92 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.106 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 91 average time/residue: 0.2183 time to fit residues: 27.9451 Evaluate side-chains 86 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0798 time to fit residues: 1.7964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8488 Z= 0.174 Angle : 0.472 7.626 11657 Z= 0.258 Chirality : 0.035 0.121 1348 Planarity : 0.003 0.048 1325 Dihedral : 19.401 176.968 1424 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.29), residues: 888 helix: 2.23 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.38 (0.39), residues: 245 *********************** 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 87 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.912 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2000 time to fit residues: 24.8268 Evaluate side-chains 81 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8488 Z= 0.178 Angle : 0.483 9.219 11657 Z= 0.262 Chirality : 0.035 0.120 1348 Planarity : 0.003 0.048 1325 Dihedral : 19.414 177.266 1424 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.29), residues: 888 helix: 2.23 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.37 (0.39), residues: 245 ********************** 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 86 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2113 time to fit residues: 25.7276 Evaluate side-chains 83 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 335 GLN E 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.104551 restraints weight = 9291.690| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.21 r_work: 0.3121 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3562 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= 0.153 Angle : 0.462 8.551 11657 Z= 0.252 Chirality : 0.034 0.119 1348 Planarity : 0.003 0.048 1325 Dihedral : 19.375 177.254 1424 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.30), residues: 888 helix: 2.34 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.28 (0.39), residues: 245 =============================================================================== Job complete usr+sys time: 1692.41 seconds wall clock time: 31 minutes 44.97 seconds (1904.97 seconds total)