Starting phenix.real_space_refine on Mon Mar 11 08:36:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/03_2024/6ln8_0927_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/03_2024/6ln8_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_0927/03_2024/6ln8_0927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/03_2024/6ln8_0927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/03_2024/6ln8_0927_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln8_0927/03_2024/6ln8_0927_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.47, per 1000 atoms: 0.58 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: 3.06 Conformation dependent library (CDL) restraints added in 1.4 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: 2.16 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: 2.62 Time building geometry restraints manager: 3.33 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: 0.250 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: 1.420 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.270 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- 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 % Allowed : 4.10 % Favored : 95.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 PHE 0.016 0.001 PHE A 759 TYR 0.015 0.001 TYR A 836 ARG 0.002 0.000 ARG A 35 *********************** 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 : 0.948 Fit side-chains REVERT: A 63 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7612 (mtm-85) REVERT: A 128 LYS cc_start: 0.8284 (mttt) cc_final: 0.8037 (mtmm) REVERT: A 140 ILE cc_start: 0.8162 (pt) cc_final: 0.7732 (pt) REVERT: A 545 MET cc_start: 0.7955 (mmm) cc_final: 0.7627 (tpp) REVERT: A 586 TYR cc_start: 0.6963 (m-10) cc_final: 0.6597 (m-80) REVERT: A 732 MET cc_start: 0.8480 (ttm) cc_final: 0.8260 (ttt) REVERT: A 816 MET cc_start: 0.7378 (mmm) cc_final: 0.6963 (mmm) REVERT: A 1028 TRP cc_start: 0.7329 (t60) cc_final: 0.6918 (t60) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2650 time to fit residues: 48.9118 Evaluate side-chains 113 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 0.0570 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: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- 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: 0.7780 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7880 Z= 0.255 Angle : 0.512 5.520 10693 Z= 0.265 Chirality : 0.041 0.140 1259 Planarity : 0.004 0.040 1362 Dihedral : 3.926 18.138 1061 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.05 % Allowed : 11.83 % Favored : 87.12 % 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: -1.29 (0.25), residues: 997 helix: -0.28 (0.22), residues: 505 sheet: -1.51 (0.44), residues: 105 loop : -1.26 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 831 HIS 0.003 0.001 HIS A 15 PHE 0.024 0.002 PHE A 759 TYR 0.015 0.002 TYR A 762 ARG 0.005 0.000 ARG A 666 *********************** 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: 9 poor density : 115 time to evaluate : 0.904 Fit side-chains REVERT: A 140 ILE cc_start: 0.8151 (pt) cc_final: 0.7697 (pt) REVERT: A 297 LYS cc_start: 0.7082 (mtpp) cc_final: 0.6770 (mttp) REVERT: A 487 PHE cc_start: 0.7721 (t80) cc_final: 0.7431 (t80) REVERT: A 545 MET cc_start: 0.7904 (mmm) cc_final: 0.7675 (tpp) REVERT: A 549 ARG cc_start: 0.7487 (mpp80) cc_final: 0.6964 (mpp80) REVERT: A 586 TYR cc_start: 0.7070 (m-10) cc_final: 0.6750 (m-80) REVERT: A 816 MET cc_start: 0.7408 (mmm) cc_final: 0.7017 (mmm) REVERT: A 1028 TRP cc_start: 0.7421 (t60) cc_final: 0.7052 (t60) outliers start: 9 outliers final: 8 residues processed: 122 average time/residue: 0.2854 time to fit residues: 45.9089 Evaluate side-chains 114 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.1354 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= 0.163 Angle : 0.461 5.390 10693 Z= 0.237 Chirality : 0.040 0.139 1259 Planarity : 0.004 0.040 1362 Dihedral : 3.782 18.922 1061 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.76 % Allowed : 13.58 % Favored : 84.66 % 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: -0.54 (0.25), residues: 997 helix: 0.47 (0.24), residues: 491 sheet: -1.35 (0.43), residues: 105 loop : -1.00 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 831 HIS 0.002 0.000 HIS A 943 PHE 0.025 0.001 PHE A 759 TYR 0.013 0.001 TYR A 836 ARG 0.003 0.000 ARG A 655 *********************** 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 129 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.091 Fit side-chains REVERT: A 120 LYS cc_start: 0.7173 (mttp) cc_final: 0.6955 (mmtp) REVERT: A 140 ILE cc_start: 0.8102 (pt) cc_final: 0.7629 (pt) REVERT: A 297 LYS cc_start: 0.7119 (mtpp) cc_final: 0.6869 (mttp) REVERT: A 487 PHE cc_start: 0.7708 (t80) cc_final: 0.7476 (t80) REVERT: A 586 TYR cc_start: 0.7061 (m-10) cc_final: 0.6768 (m-80) REVERT: A 816 MET cc_start: 0.7409 (mmm) cc_final: 0.7014 (mmm) REVERT: A 1028 TRP cc_start: 0.7431 (t60) cc_final: 0.7053 (t60) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.2505 time to fit residues: 40.8403 Evaluate side-chains 119 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1510 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= 0.195 Angle : 0.474 5.787 10693 Z= 0.243 Chirality : 0.040 0.144 1259 Planarity : 0.004 0.038 1362 Dihedral : 3.778 19.631 1061 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.22 % Allowed : 14.29 % Favored : 83.49 % 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: -0.42 (0.26), residues: 997 helix: 0.55 (0.24), residues: 502 sheet: -1.38 (0.41), residues: 115 loop : -0.91 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.002 0.000 HIS A 943 PHE 0.024 0.001 PHE A 759 TYR 0.013 0.001 TYR A 836 ARG 0.003 0.000 ARG A 666 *********************** 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 132 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.893 Fit side-chains REVERT: A 120 LYS cc_start: 0.7218 (mttp) cc_final: 0.6984 (mmtp) REVERT: A 140 ILE cc_start: 0.8135 (pt) cc_final: 0.7668 (pt) REVERT: A 297 LYS cc_start: 0.7129 (mtpp) cc_final: 0.6845 (mttp) REVERT: A 583 PHE cc_start: 0.7197 (m-80) cc_final: 0.6921 (m-80) REVERT: A 586 TYR cc_start: 0.7117 (m-10) cc_final: 0.6861 (m-80) REVERT: A 714 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: A 816 MET cc_start: 0.7464 (mmm) cc_final: 0.7032 (mmm) REVERT: A 1028 TRP cc_start: 0.7454 (t60) cc_final: 0.7070 (t60) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.2513 time to fit residues: 41.1011 Evaluate side-chains 123 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7880 Z= 0.135 Angle : 0.448 5.916 10693 Z= 0.229 Chirality : 0.039 0.142 1259 Planarity : 0.003 0.035 1362 Dihedral : 3.645 19.685 1061 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 15.34 % Favored : 82.32 % 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: -0.13 (0.26), residues: 997 helix: 0.81 (0.24), residues: 503 sheet: -1.27 (0.42), residues: 115 loop : -0.80 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 927 HIS 0.001 0.000 HIS A 943 PHE 0.024 0.001 PHE A 759 TYR 0.014 0.001 TYR A 990 ARG 0.004 0.000 ARG A 246 *********************** 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 133 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7233 (mttp) cc_final: 0.6991 (mmtp) REVERT: A 140 ILE cc_start: 0.8085 (pt) cc_final: 0.7604 (pt) REVERT: A 297 LYS cc_start: 0.7095 (mtpp) cc_final: 0.6802 (mttp) REVERT: A 575 MET cc_start: 0.5075 (mmt) cc_final: 0.4839 (tpp) REVERT: A 583 PHE cc_start: 0.7192 (m-80) cc_final: 0.6877 (m-80) REVERT: A 586 TYR cc_start: 0.7131 (m-10) cc_final: 0.6864 (m-80) REVERT: A 761 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7648 (mtp-110) REVERT: A 816 MET cc_start: 0.7449 (mmm) cc_final: 0.7061 (mmm) REVERT: A 836 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.5651 (p90) REVERT: A 1028 TRP cc_start: 0.7482 (t60) cc_final: 0.7076 (t60) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.2268 time to fit residues: 38.7991 Evaluate side-chains 122 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.0270 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7880 Z= 0.121 Angle : 0.438 6.292 10693 Z= 0.224 Chirality : 0.039 0.140 1259 Planarity : 0.003 0.037 1362 Dihedral : 3.508 19.471 1061 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 16.74 % Favored : 81.50 % 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: 0.23 (0.26), residues: 997 helix: 1.07 (0.24), residues: 504 sheet: -0.94 (0.47), residues: 105 loop : -0.66 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 854 HIS 0.001 0.000 HIS A 943 PHE 0.025 0.001 PHE A 759 TYR 0.017 0.001 TYR A 427 ARG 0.003 0.000 ARG A 246 *********************** 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 133 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.869 Fit side-chains REVERT: A 120 LYS cc_start: 0.7316 (mttp) cc_final: 0.7064 (mmtp) REVERT: A 140 ILE cc_start: 0.8051 (pt) cc_final: 0.7630 (pt) REVERT: A 143 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7455 (mtmm) REVERT: A 297 LYS cc_start: 0.7275 (mtpp) cc_final: 0.6929 (mttp) REVERT: A 479 MET cc_start: 0.6825 (ttm) cc_final: 0.6618 (ttm) REVERT: A 583 PHE cc_start: 0.7178 (m-80) cc_final: 0.6869 (m-80) REVERT: A 836 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.5650 (p90) REVERT: A 940 MET cc_start: 0.7293 (mmt) cc_final: 0.6988 (tpp) REVERT: A 1028 TRP cc_start: 0.7422 (t60) cc_final: 0.7059 (t60) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.2481 time to fit residues: 41.4307 Evaluate side-chains 124 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU 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: 4.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 428 ASN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7880 Z= 0.239 Angle : 0.494 5.422 10693 Z= 0.254 Chirality : 0.041 0.153 1259 Planarity : 0.004 0.035 1362 Dihedral : 3.719 19.924 1061 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 17.10 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 997 helix: 0.88 (0.24), residues: 500 sheet: -1.02 (0.46), residues: 105 loop : -0.62 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.003 0.001 HIS A 15 PHE 0.024 0.001 PHE A 759 TYR 0.018 0.002 TYR A 586 ARG 0.007 0.000 ARG A 863 *********************** 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 135 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.850 Fit side-chains REVERT: A 120 LYS cc_start: 0.7239 (mttp) cc_final: 0.7023 (mmtp) REVERT: A 140 ILE cc_start: 0.8138 (pt) cc_final: 0.7689 (pt) REVERT: A 297 LYS cc_start: 0.7131 (mtpp) cc_final: 0.6810 (mttp) REVERT: A 479 MET cc_start: 0.6816 (ttm) cc_final: 0.6507 (ttm) REVERT: A 498 CYS cc_start: 0.6958 (t) cc_final: 0.6170 (t) REVERT: A 583 PHE cc_start: 0.7500 (m-80) cc_final: 0.7067 (m-80) REVERT: A 586 TYR cc_start: 0.7030 (m-80) cc_final: 0.6707 (m-80) REVERT: A 714 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: A 791 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7569 (mp) REVERT: A 836 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.5637 (p90) REVERT: A 1028 TRP cc_start: 0.7490 (t60) cc_final: 0.7132 (t60) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.2350 time to fit residues: 40.4534 Evaluate side-chains 128 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.1917 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= 0.174 Angle : 0.472 5.371 10693 Z= 0.242 Chirality : 0.040 0.145 1259 Planarity : 0.004 0.035 1362 Dihedral : 3.696 19.752 1061 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.58 % Allowed : 17.45 % Favored : 79.98 % 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: 0.13 (0.26), residues: 997 helix: 0.98 (0.24), residues: 500 sheet: -1.13 (0.43), residues: 115 loop : -0.59 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.002 0.000 HIS A 943 PHE 0.023 0.001 PHE A 759 TYR 0.017 0.002 TYR A 586 ARG 0.007 0.000 ARG A 863 *********************** 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 138 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.939 Fit side-chains REVERT: A 120 LYS cc_start: 0.7246 (mttp) cc_final: 0.7027 (mmtp) REVERT: A 140 ILE cc_start: 0.8089 (pt) cc_final: 0.7660 (pt) REVERT: A 297 LYS cc_start: 0.7296 (mtpp) cc_final: 0.6941 (mttp) REVERT: A 479 MET cc_start: 0.6795 (ttm) cc_final: 0.6465 (ttm) REVERT: A 498 CYS cc_start: 0.6912 (t) cc_final: 0.6098 (t) REVERT: A 583 PHE cc_start: 0.7350 (m-80) cc_final: 0.6972 (m-80) REVERT: A 586 TYR cc_start: 0.7135 (m-80) cc_final: 0.6857 (m-80) REVERT: A 714 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: A 791 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7599 (mp) REVERT: A 836 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5646 (p90) REVERT: A 1028 TRP cc_start: 0.7491 (t60) cc_final: 0.7119 (t60) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 0.2300 time to fit residues: 40.1090 Evaluate side-chains 131 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 HIS A 542 GLN A 589 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2018 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= 0.155 Angle : 0.459 5.379 10693 Z= 0.235 Chirality : 0.040 0.143 1259 Planarity : 0.004 0.034 1362 Dihedral : 3.638 19.518 1061 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 17.56 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 997 helix: 1.01 (0.24), residues: 505 sheet: -1.11 (0.43), residues: 115 loop : -0.56 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.001 0.000 HIS A 943 PHE 0.024 0.001 PHE A 759 TYR 0.014 0.002 TYR A 586 ARG 0.007 0.000 ARG A 666 *********************** 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 133 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.881 Fit side-chains REVERT: A 120 LYS cc_start: 0.7245 (mttp) cc_final: 0.7021 (mmtp) REVERT: A 140 ILE cc_start: 0.8071 (pt) cc_final: 0.7636 (pt) REVERT: A 297 LYS cc_start: 0.7261 (mtpp) cc_final: 0.6915 (mttp) REVERT: A 479 MET cc_start: 0.6787 (ttm) cc_final: 0.6558 (ttm) REVERT: A 511 MET cc_start: 0.7321 (ttm) cc_final: 0.6962 (ttm) REVERT: A 575 MET cc_start: 0.5012 (mmt) cc_final: 0.4610 (tpp) REVERT: A 583 PHE cc_start: 0.7314 (m-80) cc_final: 0.6945 (m-80) REVERT: A 586 TYR cc_start: 0.7099 (m-80) cc_final: 0.6854 (m-80) REVERT: A 791 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7580 (mp) REVERT: A 836 TYR cc_start: 0.6704 (OUTLIER) cc_final: 0.5646 (p90) REVERT: A 1028 TRP cc_start: 0.7435 (t60) cc_final: 0.7081 (t60) outliers start: 22 outliers final: 19 residues processed: 128 average time/residue: 0.2315 time to fit residues: 38.8400 Evaluate side-chains 129 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU 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: 5.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7880 Z= 0.224 Angle : 0.495 5.414 10693 Z= 0.254 Chirality : 0.041 0.151 1259 Planarity : 0.004 0.038 1362 Dihedral : 3.778 19.793 1061 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.69 % Allowed : 17.33 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 997 helix: 0.89 (0.24), residues: 505 sheet: -1.19 (0.43), residues: 115 loop : -0.56 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.002 0.001 HIS A 943 PHE 0.023 0.001 PHE A 759 TYR 0.015 0.002 TYR A 836 ARG 0.007 0.001 ARG A 666 ********************** 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 130 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.906 Fit side-chains REVERT: A 120 LYS cc_start: 0.7239 (mttp) cc_final: 0.7031 (mmtp) REVERT: A 140 ILE cc_start: 0.8107 (pt) cc_final: 0.7662 (pt) REVERT: A 297 LYS cc_start: 0.7288 (mtpp) cc_final: 0.6929 (mttp) REVERT: A 479 MET cc_start: 0.6855 (ttm) cc_final: 0.6646 (ttm) REVERT: A 511 MET cc_start: 0.7327 (ttm) cc_final: 0.7008 (ttm) REVERT: A 575 MET cc_start: 0.5024 (mmt) cc_final: 0.4665 (tpp) REVERT: A 583 PHE cc_start: 0.7339 (m-80) cc_final: 0.6993 (m-80) REVERT: A 586 TYR cc_start: 0.7042 (m-80) cc_final: 0.6795 (m-80) REVERT: A 714 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: A 791 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7613 (mp) REVERT: A 836 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.5637 (p90) REVERT: A 1028 TRP cc_start: 0.7455 (t60) cc_final: 0.7116 (t60) outliers start: 23 outliers final: 18 residues processed: 126 average time/residue: 0.2265 time to fit residues: 37.9019 Evaluate side-chains 127 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 57 optimal weight: 7.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN 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 = 0.175201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133150 restraints weight = 8296.324| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.79 r_work: 0.3305 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7880 Z= 0.149 Angle : 0.465 5.473 10693 Z= 0.238 Chirality : 0.040 0.145 1259 Planarity : 0.004 0.034 1362 Dihedral : 3.671 19.546 1061 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 17.80 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 997 helix: 1.04 (0.24), residues: 506 sheet: -0.99 (0.46), residues: 105 loop : -0.54 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.001 0.000 HIS A 943 PHE 0.024 0.001 PHE A 759 TYR 0.014 0.002 TYR A 586 ARG 0.009 0.000 ARG A 666 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2023.19 seconds wall clock time: 37 minutes 21.59 seconds (2241.59 seconds total)