Starting phenix.real_space_refine on Sat Feb 17 17:06:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/02_2024/8d3u_27164_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/02_2024/8d3u_27164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/02_2024/8d3u_27164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/02_2024/8d3u_27164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/02_2024/8d3u_27164_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3u_27164/02_2024/8d3u_27164_neut_updated.pdb" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9272 atoms to isotropic. 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 Al 1 5.89 5 P 2 5.49 5 S 60 5.16 5 C 6462 2.51 5 N 1689 2.21 5 O 1903 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7521 Classifications: {'peptide': 971} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 929} Chain breaks: 1 Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2322 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.75, per 1000 atoms: 0.57 Number of scatterers: 10121 At special positions: 0 Unit cell: (143.59, 98.77, 131.14, 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 60 16.00 P 2 15.00 Al 1 13.00 F 4 9.00 O 1903 8.00 N 1689 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.9 seconds 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 41.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.541A pdb=" N GLN A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 120 through 152 removed outlier: 3.587A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 273 through 303 Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.871A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 522 through 538 removed outlier: 3.716A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 685 through 698 removed outlier: 3.990A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 717 Proline residue: A 713 - end of helix Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 745 through 769 removed outlier: 3.613A pdb=" N ASN A 761 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 786 removed outlier: 3.714A pdb=" N ILE A 774 " --> pdb=" O THR A 771 " (cutoff:3.500A) Proline residue: A 775 - end of helix removed outlier: 5.125A pdb=" N THR A 778 " --> pdb=" O PRO A 775 " (cutoff:3.500A) Proline residue: A 779 - end of helix removed outlier: 4.280A pdb=" N ALA A 786 " --> pdb=" O PHE A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 Processing helix chain 'A' and resid 807 through 814 removed outlier: 3.963A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 877 through 880 No H-bonds generated for 'chain 'A' and resid 877 through 880' Processing helix chain 'A' and resid 898 through 928 removed outlier: 3.804A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 937 No H-bonds generated for 'chain 'A' and resid 934 through 937' Processing helix chain 'A' and resid 942 through 960 removed outlier: 3.691A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 967 No H-bonds generated for 'chain 'A' and resid 964 through 967' Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.852A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1001 Processing helix chain 'A' and resid 1006 through 1010 Processing helix chain 'B' and resid 35 through 60 removed outlier: 3.633A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 95 through 112 removed outlier: 3.568A pdb=" N TYR B 98 " --> pdb=" O PRO B 95 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 103 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 107 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 110 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 111 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'G' and resid 37 through 57 removed outlier: 4.082A pdb=" N ILE G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU G 57 " --> pdb=" O ILE G 53 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.902A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.933A pdb=" N ILE A 720 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS A 602 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER A 365 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 604 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 380 through 382 Processing sheet with id= D, first strand: chain 'A' and resid 508 through 511 removed outlier: 6.956A pdb=" N LEU A 573 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE A 511 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE A 575 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 545 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 543 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 580 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 541 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 192 through 195 removed outlier: 3.964A pdb=" N ALA A 250 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG A 194 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL A 248 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.727A pdb=" N ALA B 260 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 87 through 91 removed outlier: 8.120A pdb=" N ILE B 88 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 298 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N PHE B 90 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU B 300 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 208 through 210 400 hydrogen bonds defined for protein. 1050 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: 2.90 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3303 1.35 - 1.46: 2297 1.46 - 1.58: 4634 1.58 - 1.70: 5 1.70 - 1.82: 92 Bond restraints: 10331 Sorted by residual: bond pdb=" C3' ADP A1101 " pdb=" C4' ADP A1101 " ideal model delta sigma weight residual 1.524 1.305 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C4' ADP A1101 " pdb=" O4' ADP A1101 " ideal model delta sigma weight residual 1.426 1.614 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" C4 ADP A1101 " pdb=" C5 ADP A1101 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" F2 ALF A1102 " pdb="AL ALF A1102 " ideal model delta sigma weight residual 1.685 1.808 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1' ADP A1101 " pdb=" O4' ADP A1101 " ideal model delta sigma weight residual 1.426 1.305 0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 10326 not shown) Histogram of bond angle deviations from ideal: 89.58 - 107.58: 385 107.58 - 125.58: 13478 125.58 - 143.58: 140 143.58 - 161.58: 0 161.58 - 179.58: 2 Bond angle restraints: 14005 Sorted by residual: angle pdb=" F3 ALF A1102 " pdb="AL ALF A1102 " pdb=" F4 ALF A1102 " ideal model delta sigma weight residual 109.63 179.58 -69.95 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F1 ALF A1102 " pdb="AL ALF A1102 " pdb=" F2 ALF A1102 " ideal model delta sigma weight residual 108.68 178.40 -69.72 3.00e+00 1.11e-01 5.40e+02 angle pdb=" N GLU A 33 " pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta sigma weight residual 110.50 130.21 -19.71 1.70e+00 3.46e-01 1.34e+02 angle pdb=" C1' ADP A1101 " pdb=" N9 ADP A1101 " pdb=" C8 ADP A1101 " ideal model delta sigma weight residual 126.00 104.64 21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" F2 ALF A1102 " pdb="AL ALF A1102 " pdb=" F4 ALF A1102 " ideal model delta sigma weight residual 110.21 89.68 20.53 3.00e+00 1.11e-01 4.68e+01 ... (remaining 14000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 5909 31.31 - 62.61: 277 62.61 - 93.92: 27 93.92 - 125.22: 0 125.22 - 156.53: 2 Dihedral angle restraints: 6215 sinusoidal: 2513 harmonic: 3702 Sorted by residual: dihedral pdb=" N GLU A 33 " pdb=" C GLU A 33 " pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta harmonic sigma weight residual 122.80 151.63 -28.83 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 49 " pdb=" CB CYS A 49 " ideal model delta sinusoidal sigma weight residual 93.00 6.73 86.27 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" C GLU A 33 " pdb=" N GLU A 33 " pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta harmonic sigma weight residual -122.60 -144.64 22.04 0 2.50e+00 1.60e-01 7.77e+01 ... (remaining 6212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1577 0.219 - 0.439: 1 0.439 - 0.658: 0 0.658 - 0.877: 0 0.877 - 1.097: 1 Chirality restraints: 1579 Sorted by residual: chirality pdb=" CA GLU A 33 " pdb=" N GLU A 33 " pdb=" C GLU A 33 " pdb=" CB GLU A 33 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CB ILE A 926 " pdb=" CA ILE A 926 " pdb=" CG1 ILE A 926 " pdb=" CG2 ILE A 926 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA MET B 121 " pdb=" N MET B 121 " pdb=" C MET B 121 " pdb=" CB MET B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1576 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 66 " -0.043 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 67 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 120 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C ASP B 120 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP B 120 " 0.015 2.00e-02 2.50e+03 pdb=" N MET B 121 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 610 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO A 611 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.027 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 2 2.09 - 2.79: 2675 2.79 - 3.50: 14626 3.50 - 4.20: 23188 4.20 - 4.90: 41978 Nonbonded interactions: 82469 Sorted by model distance: nonbonded pdb=" O TYR G 34 " pdb=" N THR G 36 " model vdw 1.392 2.520 nonbonded pdb=" O TYR G 34 " pdb=" N LEU G 37 " model vdw 2.087 2.520 nonbonded pdb=" O2B ADP A1101 " pdb=" F2 ALF A1102 " model vdw 2.149 2.390 nonbonded pdb=" O THR A 368 " pdb=" F3 ALF A1102 " model vdw 2.162 2.390 nonbonded pdb=" N ASP G 33 " pdb=" OD1 ASP G 33 " model vdw 2.174 2.520 ... (remaining 82464 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 5.180 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.160 Find NCS groups from input model: 0.260 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 10331 Z= 0.353 Angle : 1.154 69.952 14005 Z= 0.481 Chirality : 0.050 1.097 1579 Planarity : 0.004 0.064 1804 Dihedral : 17.659 156.527 3830 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 0.63 % Allowed : 27.89 % Favored : 71.48 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.61 % 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: 0.50 (0.24), residues: 1279 helix: 1.81 (0.23), residues: 539 sheet: -0.31 (0.51), residues: 121 loop : -0.88 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.002 0.001 HIS A 656 PHE 0.017 0.001 PHE G 44 TYR 0.014 0.001 TYR A 859 ARG 0.002 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ASP cc_start: 0.2422 (OUTLIER) cc_final: 0.2052 (p0) outliers start: 7 outliers final: 3 residues processed: 136 average time/residue: 0.1939 time to fit residues: 39.4939 Evaluate side-chains 132 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain G residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 283 GLN A 479 GLN A 530 ASN A 554 GLN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A 936 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 241 GLN B 265 ASN G 31 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10331 Z= 0.227 Angle : 0.576 7.525 14005 Z= 0.291 Chirality : 0.042 0.160 1579 Planarity : 0.004 0.045 1804 Dihedral : 6.227 117.183 1404 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 3.61 % Allowed : 25.81 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.38 (0.24), residues: 1279 helix: 1.66 (0.23), residues: 540 sheet: -0.38 (0.49), residues: 134 loop : -0.90 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS G 31 PHE 0.016 0.001 PHE G 44 TYR 0.016 0.001 TYR A 859 ARG 0.003 0.000 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.6852 (m-80) cc_final: 0.6475 (m-80) REVERT: A 568 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5844 (m-80) REVERT: A 750 THR cc_start: 0.9143 (p) cc_final: 0.7711 (t) REVERT: A 754 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6856 (mp0) outliers start: 40 outliers final: 18 residues processed: 169 average time/residue: 0.1765 time to fit residues: 45.4991 Evaluate side-chains 152 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 96 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 39 optimal weight: 0.0270 chunk 93 optimal weight: 4.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10331 Z= 0.162 Angle : 0.533 7.523 14005 Z= 0.271 Chirality : 0.040 0.153 1579 Planarity : 0.004 0.046 1804 Dihedral : 6.068 120.889 1396 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 2.62 % Allowed : 27.17 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.39 (0.25), residues: 1279 helix: 1.69 (0.23), residues: 538 sheet: -0.65 (0.47), residues: 138 loop : -0.84 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.002 0.000 HIS A 547 PHE 0.014 0.001 PHE G 44 TYR 0.015 0.001 TYR A 859 ARG 0.007 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 305 TYR cc_start: 0.6871 (m-80) cc_final: 0.6594 (m-80) REVERT: A 568 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: G 35 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7985 (tm-30) outliers start: 29 outliers final: 14 residues processed: 168 average time/residue: 0.1605 time to fit residues: 42.1015 Evaluate side-chains 146 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 282 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 0.0470 chunk 55 optimal weight: 0.0570 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN G 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10331 Z= 0.212 Angle : 0.555 7.458 14005 Z= 0.281 Chirality : 0.041 0.166 1579 Planarity : 0.004 0.046 1804 Dihedral : 5.961 121.404 1396 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 4.33 % Allowed : 27.08 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.33 (0.25), residues: 1279 helix: 1.58 (0.23), residues: 545 sheet: -0.61 (0.46), residues: 141 loop : -0.85 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.002 0.001 HIS G 31 PHE 0.013 0.001 PHE G 44 TYR 0.016 0.001 TYR A 859 ARG 0.005 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 305 TYR cc_start: 0.7004 (m-80) cc_final: 0.6572 (m-80) REVERT: A 568 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5748 (m-80) REVERT: A 1008 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: G 35 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7880 (pp30) outliers start: 48 outliers final: 25 residues processed: 176 average time/residue: 0.1594 time to fit residues: 43.9988 Evaluate side-chains 154 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 0.051 10331 Z= 0.191 Angle : 0.558 8.489 14005 Z= 0.280 Chirality : 0.041 0.188 1579 Planarity : 0.004 0.045 1804 Dihedral : 5.769 116.007 1396 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 3.70 % Allowed : 26.99 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.38 (0.25), residues: 1279 helix: 1.63 (0.23), residues: 544 sheet: -0.60 (0.47), residues: 139 loop : -0.83 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.004 0.001 HIS A 199 PHE 0.022 0.001 PHE A 291 TYR 0.015 0.001 TYR A 859 ARG 0.003 0.000 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 305 TYR cc_start: 0.6987 (m-80) cc_final: 0.6598 (m-80) REVERT: A 568 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.5760 (m-80) REVERT: A 950 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 1008 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: B 202 MET cc_start: 0.4393 (tpt) cc_final: 0.3781 (tmm) outliers start: 41 outliers final: 25 residues processed: 166 average time/residue: 0.1676 time to fit residues: 43.2360 Evaluate side-chains 160 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 123 optimal weight: 0.0170 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 491 ASN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10331 Z= 0.167 Angle : 0.554 8.160 14005 Z= 0.277 Chirality : 0.041 0.174 1579 Planarity : 0.004 0.046 1804 Dihedral : 5.490 110.305 1396 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 3.97 % Allowed : 26.53 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.39 (0.25), residues: 1279 helix: 1.65 (0.23), residues: 545 sheet: -0.55 (0.47), residues: 137 loop : -0.86 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.002 0.001 HIS A 483 PHE 0.011 0.001 PHE G 44 TYR 0.015 0.001 TYR A 859 ARG 0.005 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 305 TYR cc_start: 0.6983 (m-80) cc_final: 0.6589 (m-80) REVERT: A 568 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5691 (m-80) REVERT: A 1008 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7874 (tt0) outliers start: 44 outliers final: 29 residues processed: 175 average time/residue: 0.1676 time to fit residues: 45.1634 Evaluate side-chains 167 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.0000 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 667 GLN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10331 Z= 0.214 Angle : 0.581 7.988 14005 Z= 0.288 Chirality : 0.042 0.195 1579 Planarity : 0.004 0.045 1804 Dihedral : 5.498 111.440 1396 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 4.60 % Allowed : 26.62 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.37 (0.25), residues: 1279 helix: 1.65 (0.23), residues: 545 sheet: -0.49 (0.47), residues: 138 loop : -0.91 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.002 0.000 HIS A 656 PHE 0.020 0.001 PHE A 946 TYR 0.016 0.001 TYR A 859 ARG 0.004 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 137 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 305 TYR cc_start: 0.7095 (m-80) cc_final: 0.6666 (m-80) REVERT: A 568 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5772 (m-80) REVERT: A 754 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 901 ARG cc_start: 0.8849 (ptp90) cc_final: 0.8228 (ptt-90) REVERT: A 1008 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7911 (tt0) outliers start: 51 outliers final: 39 residues processed: 169 average time/residue: 0.1669 time to fit residues: 44.1534 Evaluate side-chains 172 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 0.0470 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 0.0000 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN B 181 ASN B 241 GLN G 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10331 Z= 0.153 Angle : 0.573 9.124 14005 Z= 0.281 Chirality : 0.041 0.229 1579 Planarity : 0.004 0.045 1804 Dihedral : 5.361 108.850 1396 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.53 % Favored : 95.39 % Rotamer: Outliers : 3.34 % Allowed : 27.71 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.45 (0.25), residues: 1279 helix: 1.71 (0.23), residues: 543 sheet: -0.17 (0.50), residues: 127 loop : -0.91 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 PHE 0.015 0.001 PHE A 291 TYR 0.014 0.001 TYR A 859 ARG 0.003 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 303 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8782 (mm) REVERT: A 568 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: A 806 MET cc_start: 0.8231 (tpt) cc_final: 0.7929 (tpt) REVERT: A 946 PHE cc_start: 0.8061 (t80) cc_final: 0.7807 (t80) REVERT: A 1008 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7842 (tt0) outliers start: 37 outliers final: 28 residues processed: 169 average time/residue: 0.1470 time to fit residues: 39.5580 Evaluate side-chains 167 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 282 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 0.0670 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 473 ASN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN B 241 GLN G 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10331 Z= 0.158 Angle : 0.568 8.664 14005 Z= 0.278 Chirality : 0.041 0.211 1579 Planarity : 0.004 0.046 1804 Dihedral : 5.261 106.740 1396 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 3.43 % Allowed : 27.89 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.48 (0.25), residues: 1279 helix: 1.78 (0.23), residues: 538 sheet: -0.14 (0.51), residues: 126 loop : -0.93 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.002 0.001 HIS A 656 PHE 0.010 0.001 PHE G 44 TYR 0.014 0.001 TYR A 859 ARG 0.003 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 568 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5652 (m-80) REVERT: A 717 LYS cc_start: 0.8601 (tppt) cc_final: 0.8310 (tppt) REVERT: A 806 MET cc_start: 0.8261 (tpt) cc_final: 0.7986 (tpt) REVERT: A 822 MET cc_start: 0.8148 (mmm) cc_final: 0.7927 (tpp) REVERT: A 946 PHE cc_start: 0.8142 (t80) cc_final: 0.7942 (t80) outliers start: 38 outliers final: 29 residues processed: 166 average time/residue: 0.1660 time to fit residues: 43.7389 Evaluate side-chains 168 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 282 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 473 ASN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN G 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10331 Z= 0.196 Angle : 0.587 8.156 14005 Z= 0.287 Chirality : 0.042 0.227 1579 Planarity : 0.004 0.046 1804 Dihedral : 5.267 106.915 1396 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 3.25 % Allowed : 28.34 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.43 (0.25), residues: 1279 helix: 1.72 (0.23), residues: 539 sheet: -0.14 (0.50), residues: 128 loop : -0.96 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS A 656 PHE 0.011 0.001 PHE G 44 TYR 0.016 0.001 TYR A 859 ARG 0.002 0.000 ARG B 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2558 Ramachandran restraints generated. 1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 568 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.5800 (m-80) REVERT: A 754 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: A 822 MET cc_start: 0.8242 (mmm) cc_final: 0.8002 (tpp) REVERT: B 87 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6966 (pm20) outliers start: 36 outliers final: 31 residues processed: 164 average time/residue: 0.1520 time to fit residues: 39.6956 Evaluate side-chains 169 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 282 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 chunk 18 optimal weight: 0.0970 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 473 ASN ** A 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN B 241 GLN G 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.108471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088563 restraints weight = 22269.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091804 restraints weight = 12091.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093398 restraints weight = 7368.832| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10331 Z= 0.147 Angle : 0.572 8.151 14005 Z= 0.280 Chirality : 0.041 0.221 1579 Planarity : 0.004 0.045 1804 Dihedral : 5.120 101.703 1396 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 2.98 % Allowed : 29.42 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.46 (0.24), residues: 1279 helix: 1.76 (0.23), residues: 539 sheet: -0.13 (0.50), residues: 126 loop : -0.95 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.002 0.001 HIS A 909 PHE 0.026 0.001 PHE A 946 TYR 0.014 0.001 TYR A 859 ARG 0.002 0.000 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.02 seconds wall clock time: 40 minutes 12.06 seconds (2412.06 seconds total)