Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 15:15:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/04_2023/6ln8_0927_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/04_2023/6ln8_0927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/04_2023/6ln8_0927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/04_2023/6ln8_0927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/04_2023/6ln8_0927_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/04_2023/6ln8_0927_updated.pdb" } resolution = 3.1 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= 0.007 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 57 5.16 5 Be 1 3.05 5 C 4932 2.51 5 N 1294 2.21 5 O 1451 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ASP 490": "OD1" <-> "OD2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A ASP 579": "OD1" <-> "OD2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 859": "OD1" <-> "OD2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 878": "OD1" <-> "OD2" Residue "A ASP 881": "OD1" <-> "OD2" Residue "A PHE 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7739 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7739 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'peptide': 1003, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 957, None: 2} Not linked: pdbres="SER A1031 " pdbres="BEF A2001 " Not linked: pdbres="BEF A2001 " pdbres=" MG A2002 " Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 4.75, per 1000 atoms: 0.61 Number of scatterers: 7739 At special positions: 0 Unit cell: (88.395, 92.13, 145.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 57 16.00 Mg 1 11.99 F 3 9.00 O 1451 8.00 N 1294 7.00 C 4932 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 7 sheets defined 47.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 9 through 15 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.677A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 76 Processing helix chain 'A' and resid 85 through 117 removed outlier: 5.083A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 248 through 275 Processing helix chain 'A' and resid 288 through 305 removed outlier: 4.371A pdb=" N ILE A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.707A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 420 Processing helix chain 'A' and resid 440 through 451 removed outlier: 4.468A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.728A pdb=" N GLU A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.735A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.739A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 710 Proline residue: A 708 - end of helix Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 740 through 780 removed outlier: 3.764A pdb=" N TYR A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 808 removed outlier: 3.938A pdb=" N TRP A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix removed outlier: 3.893A pdb=" N GLY A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.844A pdb=" N ILE A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 888 through 891 Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 948 Processing helix chain 'A' and resid 952 through 955 No H-bonds generated for 'chain 'A' and resid 952 through 955' Processing helix chain 'A' and resid 963 through 989 Proline residue: A 975 - end of helix removed outlier: 3.981A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 Proline residue: A1024 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 150 through 154 removed outlier: 6.859A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.479A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.520A pdb=" N ILE A 715 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 428 Processing sheet with id= F, first strand: chain 'A' and resid 479 through 481 removed outlier: 3.558A pdb=" N THR A 499 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR A 565 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE A 592 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 15.736A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 14.642A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.835A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A 592 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL A 529 " --> pdb=" O PHE A 592 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2532 1.34 - 1.46: 1398 1.46 - 1.58: 3862 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7880 Sorted by residual: bond pdb=" BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" BE BEF A2001 " pdb=" F1 BEF A2001 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C ASP A 398 " pdb=" O ASP A 398 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.30e-02 5.92e+03 9.31e-01 bond pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.55e-02 4.16e+03 6.89e-01 ... (remaining 7875 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 237 106.95 - 113.71: 4532 113.71 - 120.47: 3046 120.47 - 127.24: 2793 127.24 - 134.00: 85 Bond angle restraints: 10693 Sorted by residual: angle pdb=" F2 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 119.96 106.06 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" F1 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 120.12 109.98 10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N ASP A 398 " pdb=" CA ASP A 398 " pdb=" C ASP A 398 " ideal model delta sigma weight residual 112.13 107.72 4.41 1.37e+00 5.33e-01 1.04e+01 angle pdb=" N THR A 358 " pdb=" CA THR A 358 " pdb=" C THR A 358 " ideal model delta sigma weight residual 110.53 106.96 3.57 1.29e+00 6.01e-01 7.65e+00 angle pdb=" F1 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 119.91 112.30 7.61 3.00e+00 1.11e-01 6.44e+00 ... (remaining 10688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4279 16.00 - 32.01: 397 32.01 - 48.01: 89 48.01 - 64.01: 7 64.01 - 80.01: 5 Dihedral angle restraints: 4777 sinusoidal: 1882 harmonic: 2895 Sorted by residual: dihedral pdb=" CA LEU A 947 " pdb=" C LEU A 947 " pdb=" N TYR A 948 " pdb=" CA TYR A 948 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR A 357 " pdb=" C THR A 357 " pdb=" N THR A 358 " pdb=" CA THR A 358 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CB MET A 908 " pdb=" CG MET A 908 " pdb=" SD MET A 908 " pdb=" CE MET A 908 " ideal model delta sinusoidal sigma weight residual 60.00 112.21 -52.21 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 735 0.027 - 0.055: 345 0.055 - 0.082: 102 0.082 - 0.110: 60 0.110 - 0.137: 17 Chirality restraints: 1259 Sorted by residual: chirality pdb=" CA ILE A 307 " pdb=" N ILE A 307 " pdb=" C ILE A 307 " pdb=" CB ILE A 307 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 621 " pdb=" N ILE A 621 " pdb=" C ILE A 621 " pdb=" CB ILE A 621 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1256 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 975 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU A 796 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 952 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 953 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 953 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 953 " 0.021 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 66 2.62 - 3.19: 7073 3.19 - 3.76: 12083 3.76 - 4.33: 17095 4.33 - 4.90: 28164 Nonbonded interactions: 64481 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.051 2.170 nonbonded pdb=" F1 BEF A2001 " pdb="MG MG A2002 " model vdw 2.059 2.120 nonbonded pdb=" OD2 ASP A 351 " pdb=" F1 BEF A2001 " model vdw 2.085 2.390 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.097 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.101 2.170 ... (remaining 64476 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: 0.280 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: 1.790 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 24.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 7880 Z= 0.205 Angle : 0.562 13.901 10693 Z= 0.320 Chirality : 0.039 0.137 1259 Planarity : 0.004 0.041 1362 Dihedral : 12.814 80.014 2901 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -2.71 (0.22), residues: 997 helix: -1.61 (0.20), residues: 506 sheet: -1.80 (0.43), residues: 105 loop : -1.82 (0.26), residues: 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.960 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2731 time to fit residues: 50.2404 Evaluate side-chains 112 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 132 GLN A 177 GLN A 428 ASN A 582 ASN A 615 GLN A 671 ASN A 682 HIS A 868 GLN A 943 HIS A 965 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7880 Z= 0.270 Angle : 0.525 5.582 10693 Z= 0.271 Chirality : 0.042 0.139 1259 Planarity : 0.004 0.040 1362 Dihedral : 3.965 18.121 1061 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 997 helix: -0.24 (0.23), residues: 498 sheet: -1.51 (0.44), residues: 105 loop : -1.22 (0.28), residues: 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.975 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 122 average time/residue: 0.2466 time to fit residues: 39.5433 Evaluate side-chains 116 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0824 time to fit residues: 2.7762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.0000 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7880 Z= 0.152 Angle : 0.464 5.646 10693 Z= 0.239 Chirality : 0.040 0.138 1259 Planarity : 0.004 0.041 1362 Dihedral : 3.759 18.821 1061 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.70 % 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: -0.41 (0.26), residues: 997 helix: 0.59 (0.24), residues: 484 sheet: -1.29 (0.44), residues: 105 loop : -0.94 (0.28), residues: 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.975 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 120 average time/residue: 0.2498 time to fit residues: 39.1556 Evaluate side-chains 112 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0696 time to fit residues: 1.7349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7880 Z= 0.169 Angle : 0.466 5.771 10693 Z= 0.240 Chirality : 0.040 0.142 1259 Planarity : 0.003 0.039 1362 Dihedral : 3.730 19.504 1061 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.70 % 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: -0.22 (0.26), residues: 997 helix: 0.74 (0.24), residues: 495 sheet: -1.27 (0.42), residues: 115 loop : -0.84 (0.29), residues: 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.969 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 119 average time/residue: 0.2530 time to fit residues: 39.3536 Evaluate side-chains 110 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0768 time to fit residues: 1.6159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0000 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 542 GLN ** A 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 7880 Z= 0.228 Angle : 0.497 6.018 10693 Z= 0.255 Chirality : 0.041 0.153 1259 Planarity : 0.004 0.035 1362 Dihedral : 3.842 19.927 1061 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 997 helix: 0.73 (0.24), residues: 495 sheet: -1.31 (0.42), residues: 115 loop : -0.78 (0.29), residues: 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.976 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 0.2583 time to fit residues: 42.3710 Evaluate side-chains 117 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1097 time to fit residues: 2.2228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 80 optimal weight: 0.0000 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN A 589 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 7880 Z= 0.132 Angle : 0.452 6.160 10693 Z= 0.232 Chirality : 0.039 0.145 1259 Planarity : 0.003 0.035 1362 Dihedral : 3.682 19.624 1061 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.47 % 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: 0.04 (0.26), residues: 997 helix: 0.95 (0.24), residues: 503 sheet: -1.21 (0.43), residues: 115 loop : -0.73 (0.30), residues: 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.992 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 118 average time/residue: 0.2586 time to fit residues: 39.8377 Evaluate side-chains 110 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0913 time to fit residues: 1.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7880 Z= 0.170 Angle : 0.479 7.548 10693 Z= 0.246 Chirality : 0.040 0.148 1259 Planarity : 0.003 0.037 1362 Dihedral : 3.731 19.888 1061 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.05 % 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: 0.05 (0.26), residues: 997 helix: 0.93 (0.24), residues: 504 sheet: -1.19 (0.42), residues: 115 loop : -0.67 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.955 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.2546 time to fit residues: 39.6784 Evaluate side-chains 116 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0711 time to fit residues: 1.7570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7880 Z= 0.221 Angle : 0.509 7.006 10693 Z= 0.259 Chirality : 0.041 0.150 1259 Planarity : 0.004 0.036 1362 Dihedral : 3.866 20.051 1061 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.35 % 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: -0.02 (0.26), residues: 997 helix: 0.84 (0.24), residues: 503 sheet: -1.24 (0.42), residues: 115 loop : -0.64 (0.30), residues: 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.997 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 116 average time/residue: 0.2649 time to fit residues: 40.1405 Evaluate side-chains 112 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0758 time to fit residues: 1.6203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 0.1980 chunk 57 optimal weight: 10.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 396 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7880 Z= 0.160 Angle : 0.479 6.847 10693 Z= 0.246 Chirality : 0.040 0.153 1259 Planarity : 0.003 0.035 1362 Dihedral : 3.775 19.810 1061 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 997 helix: 0.97 (0.24), residues: 504 sheet: -1.17 (0.43), residues: 115 loop : -0.62 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.044 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.2665 time to fit residues: 39.5430 Evaluate side-chains 109 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7880 Z= 0.182 Angle : 0.493 6.804 10693 Z= 0.253 Chirality : 0.041 0.147 1259 Planarity : 0.003 0.035 1362 Dihedral : 3.826 19.831 1061 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 997 helix: 0.95 (0.24), residues: 502 sheet: -1.23 (0.42), residues: 115 loop : -0.59 (0.30), residues: 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.131 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.2749 time to fit residues: 41.5303 Evaluate side-chains 113 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.174992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132848 restraints weight = 8347.924| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.81 r_work: 0.3263 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7880 Z= 0.180 Angle : 0.497 6.691 10693 Z= 0.255 Chirality : 0.041 0.146 1259 Planarity : 0.004 0.035 1362 Dihedral : 3.810 19.553 1061 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 997 helix: 0.96 (0.24), residues: 503 sheet: -1.19 (0.42), residues: 115 loop : -0.59 (0.31), residues: 379 =============================================================================== Job complete usr+sys time: 1922.61 seconds wall clock time: 35 minutes 29.74 seconds (2129.74 seconds total)