Starting phenix.real_space_refine on Mon Sep 23 23:59:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7h_22699/09_2024/7k7h_22699.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7h_22699/09_2024/7k7h_22699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7h_22699/09_2024/7k7h_22699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7h_22699/09_2024/7k7h_22699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7h_22699/09_2024/7k7h_22699.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7h_22699/09_2024/7k7h_22699.cif" } resolution = 3.0 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= 0.001 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4019 2.51 5 N 1045 2.21 5 O 1226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6323 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 110} Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Time building chain proxies: 4.35, per 1000 atoms: 0.69 Number of scatterers: 6323 At special positions: 0 Unit cell: (83, 107.07, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1226 8.00 N 1045 7.00 C 4019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 70 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 133 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.50 Conformation dependent library (CDL) restraints added in 906.2 milliseconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1526 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 16.7% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.541A pdb=" N TYR A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 95 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.558A pdb=" N ASN B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.619A pdb=" N SER C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'D' and resid 81 through 96 Processing helix chain 'D' and resid 110 through 117 removed outlier: 3.527A pdb=" N VAL D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 96 Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.045A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 241 removed outlier: 4.120A pdb=" N VAL G 235 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 239 " --> pdb=" O VAL G 235 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.719A pdb=" N ALA A 69 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 55 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN A 46 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 52 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 44 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS A 54 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 42 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 56 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR A 33 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL A 103 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER A 35 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 101 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN A 104 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU A 122 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 104 removed outlier: 4.869A pdb=" N VAL B 99 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP B 36 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS B 56 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 42 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 54 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 44 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR B 52 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 122 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS B 70 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY B 124 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 12.444A pdb=" N VAL B 72 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 123 " --> pdb=" O HIS B 102 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS B 102 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 125 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 100 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 46 removed outlier: 6.392A pdb=" N LEU B 42 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 127 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 44 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 46 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL E 123 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU E 122 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN E 104 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 124 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS E 102 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE E 101 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER E 35 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL E 103 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR E 33 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU E 42 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN E 46 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL D 123 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N HIS D 102 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 125 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG D 100 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE D 101 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER D 35 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL D 103 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR D 33 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS D 56 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU D 42 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS D 54 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL D 44 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR D 52 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 55 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 121 through 127 removed outlier: 6.495A pdb=" N LEU E 122 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS E 70 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N GLY E 124 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 12.809A pdb=" N VAL E 72 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 17.849A pdb=" N SER E 126 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 55 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR E 52 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL E 44 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS E 54 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU E 42 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS E 56 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 127 through 128 removed outlier: 4.000A pdb=" N SER B 127 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE B 134 " --> pdb=" O SER B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA7, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.806A pdb=" N TYR C 52 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL C 44 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 54 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 42 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 56 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU C 125 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS C 102 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.710A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.820A pdb=" N LYS L 36 " --> pdb=" O ASN L 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 51 through 52 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.865A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.520A pdb=" N SER H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AB6, first strand: chain 'H' and resid 98 through 100 removed outlier: 7.181A pdb=" N GLY H 98 " --> pdb=" O PRO H 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 456 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: 1.44 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1971 1.34 - 1.46: 1246 1.46 - 1.57: 3225 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6480 Sorted by residual: bond pdb=" C SER C 50 " pdb=" N PRO C 51 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" N TYR C 52 " pdb=" CA TYR C 52 " ideal model delta sigma weight residual 1.454 1.482 -0.029 1.23e-02 6.61e+03 5.45e+00 bond pdb=" N PHE C 53 " pdb=" CA PHE C 53 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.26e-02 6.30e+03 4.54e+00 bond pdb=" N TYR A 52 " pdb=" CA TYR A 52 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.20e-02 6.94e+03 3.34e+00 bond pdb=" N PRO C 51 " pdb=" CD PRO C 51 " ideal model delta sigma weight residual 1.473 1.493 -0.020 1.40e-02 5.10e+03 2.07e+00 ... (remaining 6475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 8499 1.26 - 2.51: 256 2.51 - 3.77: 44 3.77 - 5.02: 7 5.02 - 6.28: 6 Bond angle restraints: 8812 Sorted by residual: angle pdb=" N PRO C 51 " pdb=" CA PRO C 51 " pdb=" CB PRO C 51 " ideal model delta sigma weight residual 103.27 106.35 -3.08 9.00e-01 1.23e+00 1.17e+01 angle pdb=" C PHE C 53 " pdb=" CA PHE C 53 " pdb=" CB PHE C 53 " ideal model delta sigma weight residual 109.65 114.68 -5.03 1.75e+00 3.27e-01 8.25e+00 angle pdb=" CA PRO C 51 " pdb=" N PRO C 51 " pdb=" CD PRO C 51 " ideal model delta sigma weight residual 112.00 108.45 3.55 1.40e+00 5.10e-01 6.43e+00 angle pdb=" N ASN E 61 " pdb=" CA ASN E 61 " pdb=" C ASN E 61 " ideal model delta sigma weight residual 114.04 110.97 3.07 1.24e+00 6.50e-01 6.15e+00 angle pdb=" CA TYR C 52 " pdb=" C TYR C 52 " pdb=" O TYR C 52 " ideal model delta sigma weight residual 121.46 118.72 2.74 1.17e+00 7.31e-01 5.49e+00 ... (remaining 8807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3465 17.94 - 35.88: 294 35.88 - 53.83: 48 53.83 - 71.77: 4 71.77 - 89.71: 4 Dihedral angle restraints: 3815 sinusoidal: 1437 harmonic: 2378 Sorted by residual: dihedral pdb=" CA ASN A 61 " pdb=" C ASN A 61 " pdb=" N GLY A 62 " pdb=" CA GLY A 62 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " pdb=" CD LYS H 43 " pdb=" CE LYS H 43 " ideal model delta sinusoidal sigma weight residual 60.00 105.17 -45.17 3 1.50e+01 4.44e-03 8.12e+00 dihedral pdb=" CG ARG L 67 " pdb=" CD ARG L 67 " pdb=" NE ARG L 67 " pdb=" CZ ARG L 67 " ideal model delta sinusoidal sigma weight residual -90.00 -51.95 -38.05 2 1.50e+01 4.44e-03 8.10e+00 ... (remaining 3812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 470 0.025 - 0.049: 295 0.049 - 0.074: 117 0.074 - 0.099: 61 0.099 - 0.123: 35 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL B 99 " pdb=" N VAL B 99 " pdb=" C VAL B 99 " pdb=" CB VAL B 99 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL E 38 " pdb=" N VAL E 38 " pdb=" C VAL E 38 " pdb=" CB VAL E 38 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 975 not shown) Planarity restraints: 1115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 52 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C TYR A 52 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR A 52 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 53 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 79 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO C 80 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 52 " 0.006 2.00e-02 2.50e+03 1.03e-02 2.13e+00 pdb=" CG TYR A 52 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 52 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 52 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 52 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 52 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 52 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 52 " -0.009 2.00e-02 2.50e+03 ... (remaining 1112 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1864 2.80 - 3.33: 5392 3.33 - 3.85: 10098 3.85 - 4.38: 12418 4.38 - 4.90: 22031 Nonbonded interactions: 51803 Sorted by model distance: nonbonded pdb=" O THR C 26 " pdb=" ND2 ASN C 31 " model vdw 2.281 3.120 nonbonded pdb=" OE1 GLN A 46 " pdb=" OG SER B 81 " model vdw 2.285 3.040 nonbonded pdb=" O LEU E 112 " pdb=" OG1 THR E 116 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR E 131 " pdb=" OE1 GLN E 132 " model vdw 2.305 3.040 nonbonded pdb=" OG SER C 40 " pdb=" OE1 GLU C 41 " model vdw 2.310 3.040 ... (remaining 51798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.50 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: 3.020 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 0.038 6480 Z= 0.218 Angle : 0.538 6.281 8812 Z= 0.300 Chirality : 0.043 0.123 978 Planarity : 0.004 0.039 1115 Dihedral : 13.308 89.709 2265 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -5.02 (0.23), residues: 800 helix: -4.10 (0.22), residues: 125 sheet: -2.98 (0.27), residues: 259 loop : -3.31 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 78 HIS 0.003 0.001 HIS D 102 PHE 0.011 0.001 PHE L 77 TYR 0.020 0.001 TYR A 52 ARG 0.005 0.000 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7701 (pm20) cc_final: 0.7437 (pm20) REVERT: L 84 VAL cc_start: 0.8442 (p) cc_final: 0.8170 (m) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.8480 time to fit residues: 235.9823 Evaluate side-chains 199 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 88 GLN D 29 ASN D 102 HIS E 88 GLN E 115 ASN H 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6480 Z= 0.475 Angle : 0.690 5.767 8812 Z= 0.373 Chirality : 0.048 0.161 978 Planarity : 0.005 0.036 1115 Dihedral : 4.647 19.779 870 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.84 % Allowed : 22.05 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.69 (0.27), residues: 800 helix: -2.44 (0.34), residues: 150 sheet: -2.24 (0.29), residues: 264 loop : -2.51 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 78 HIS 0.006 0.001 HIS B 102 PHE 0.015 0.002 PHE D 117 TYR 0.021 0.002 TYR C 91 ARG 0.007 0.001 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 206 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: H 66 ASP cc_start: 0.6667 (p0) cc_final: 0.6461 (p0) REVERT: H 87 THR cc_start: 0.8442 (t) cc_final: 0.7162 (t) outliers start: 34 outliers final: 16 residues processed: 223 average time/residue: 0.8720 time to fit residues: 206.3110 Evaluate side-chains 205 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN D 29 ASN E 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6480 Z= 0.201 Angle : 0.597 7.061 8812 Z= 0.317 Chirality : 0.045 0.158 978 Planarity : 0.003 0.031 1115 Dihedral : 4.240 20.877 870 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.55 % Allowed : 22.76 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.94 (0.28), residues: 800 helix: -1.25 (0.40), residues: 150 sheet: -1.91 (0.31), residues: 254 loop : -2.20 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 78 HIS 0.002 0.001 HIS B 43 PHE 0.012 0.001 PHE D 117 TYR 0.013 0.001 TYR E 110 ARG 0.004 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6585 (mtpp) REVERT: D 133 CYS cc_start: 0.4671 (m) cc_final: 0.4339 (m) outliers start: 39 outliers final: 18 residues processed: 227 average time/residue: 0.8217 time to fit residues: 198.5448 Evaluate side-chains 210 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 81 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN D 29 ASN E 88 GLN E 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6480 Z= 0.217 Angle : 0.598 6.675 8812 Z= 0.315 Chirality : 0.045 0.161 978 Planarity : 0.003 0.029 1115 Dihedral : 4.117 17.559 870 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.55 % Allowed : 24.75 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.63 (0.29), residues: 800 helix: -0.63 (0.43), residues: 150 sheet: -1.75 (0.29), residues: 305 loop : -2.12 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 78 HIS 0.002 0.001 HIS B 43 PHE 0.012 0.001 PHE D 117 TYR 0.015 0.001 TYR H 60 ARG 0.003 0.000 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6591 (mtpp) REVERT: C 106 ASN cc_start: 0.7946 (m110) cc_final: 0.7636 (m110) outliers start: 39 outliers final: 22 residues processed: 212 average time/residue: 0.8330 time to fit residues: 188.3854 Evaluate side-chains 210 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN B 106 ASN L 6 GLN H 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6480 Z= 0.193 Angle : 0.603 8.303 8812 Z= 0.314 Chirality : 0.045 0.161 978 Planarity : 0.003 0.031 1115 Dihedral : 3.991 18.017 870 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.55 % Allowed : 28.02 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.27 (0.29), residues: 800 helix: -0.23 (0.44), residues: 150 sheet: -1.44 (0.30), residues: 299 loop : -2.03 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 108 HIS 0.003 0.001 HIS B 43 PHE 0.012 0.001 PHE E 92 TYR 0.009 0.001 TYR H 107 ARG 0.002 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6572 (mtpp) REVERT: E 41 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7543 (mm-30) outliers start: 39 outliers final: 17 residues processed: 211 average time/residue: 0.8311 time to fit residues: 186.9783 Evaluate side-chains 199 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6480 Z= 0.344 Angle : 0.690 10.286 8812 Z= 0.359 Chirality : 0.047 0.158 978 Planarity : 0.004 0.050 1115 Dihedral : 4.438 20.063 870 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.98 % Allowed : 28.59 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.17 (0.28), residues: 800 helix: 0.35 (0.46), residues: 120 sheet: -1.34 (0.32), residues: 265 loop : -2.05 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 108 HIS 0.004 0.001 HIS B 102 PHE 0.013 0.002 PHE D 117 TYR 0.016 0.002 TYR H 82 ARG 0.003 0.001 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: C 106 ASN cc_start: 0.7992 (m110) cc_final: 0.7783 (m110) outliers start: 35 outliers final: 21 residues processed: 207 average time/residue: 0.6801 time to fit residues: 150.2891 Evaluate side-chains 202 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN D 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6480 Z= 0.215 Angle : 0.666 11.057 8812 Z= 0.344 Chirality : 0.046 0.195 978 Planarity : 0.003 0.027 1115 Dihedral : 4.209 19.796 870 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.41 % Allowed : 30.87 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.99 (0.29), residues: 800 helix: -0.15 (0.44), residues: 150 sheet: -1.12 (0.31), residues: 294 loop : -1.93 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 108 HIS 0.003 0.001 HIS B 43 PHE 0.014 0.001 PHE D 117 TYR 0.011 0.001 TYR H 107 ARG 0.002 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7649 (mm-30) outliers start: 24 outliers final: 18 residues processed: 211 average time/residue: 0.8347 time to fit residues: 187.1105 Evaluate side-chains 201 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 81 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN D 61 ASN E 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6480 Z= 0.220 Angle : 0.668 11.324 8812 Z= 0.349 Chirality : 0.046 0.197 978 Planarity : 0.004 0.071 1115 Dihedral : 4.174 20.554 870 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.27 % Allowed : 33.00 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.86 (0.29), residues: 800 helix: -0.04 (0.44), residues: 150 sheet: -1.05 (0.31), residues: 294 loop : -1.85 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 108 HIS 0.003 0.001 HIS A 43 PHE 0.016 0.001 PHE D 117 TYR 0.016 0.001 TYR H 60 ARG 0.006 0.000 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 CYS cc_start: 0.5206 (m) cc_final: 0.4738 (m) REVERT: E 41 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7636 (mm-30) outliers start: 23 outliers final: 16 residues processed: 200 average time/residue: 0.8533 time to fit residues: 181.5434 Evaluate side-chains 200 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 81 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6480 Z= 0.217 Angle : 0.698 11.074 8812 Z= 0.361 Chirality : 0.046 0.199 978 Planarity : 0.003 0.025 1115 Dihedral : 4.135 20.436 870 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.99 % Allowed : 34.28 % Favored : 62.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.29), residues: 800 helix: 0.66 (0.46), residues: 120 sheet: -0.99 (0.31), residues: 298 loop : -2.07 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 108 HIS 0.003 0.001 HIS A 102 PHE 0.016 0.001 PHE D 117 TYR 0.015 0.001 TYR E 34 ARG 0.003 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 CYS cc_start: 0.5175 (m) cc_final: 0.4699 (m) REVERT: E 41 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7645 (mm-30) outliers start: 21 outliers final: 15 residues processed: 201 average time/residue: 0.7580 time to fit residues: 162.9875 Evaluate side-chains 195 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 0.0010 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6480 Z= 0.267 Angle : 0.736 11.860 8812 Z= 0.384 Chirality : 0.047 0.251 978 Planarity : 0.003 0.024 1115 Dihedral : 4.329 20.883 870 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.56 % Allowed : 34.57 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.90 (0.29), residues: 800 helix: 0.64 (0.47), residues: 120 sheet: -1.06 (0.30), residues: 301 loop : -2.05 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 78 HIS 0.003 0.001 HIS A 102 PHE 0.015 0.001 PHE D 117 TYR 0.019 0.001 TYR H 82 ARG 0.003 0.000 ARG L 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 CYS cc_start: 0.5220 (m) cc_final: 0.4718 (m) REVERT: E 41 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7705 (mm-30) outliers start: 18 outliers final: 16 residues processed: 193 average time/residue: 0.8701 time to fit residues: 179.1697 Evaluate side-chains 194 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain H residue 81 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.086833 restraints weight = 12057.214| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.32 r_work: 0.3092 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6480 Z= 0.253 Angle : 0.741 11.016 8812 Z= 0.384 Chirality : 0.047 0.193 978 Planarity : 0.003 0.023 1115 Dihedral : 4.326 20.422 870 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.13 % Allowed : 34.42 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.29), residues: 800 helix: 0.70 (0.47), residues: 120 sheet: -1.01 (0.30), residues: 297 loop : -2.06 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.003 0.001 HIS A 102 PHE 0.015 0.001 PHE D 117 TYR 0.016 0.001 TYR E 34 ARG 0.003 0.000 ARG L 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3192.55 seconds wall clock time: 64 minutes 29.71 seconds (3869.71 seconds total)