Starting phenix.real_space_refine on Thu Sep 26 22:27:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/09_2024/8sn7_40615.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/09_2024/8sn7_40615.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/8sn7_40615/09_2024/8sn7_40615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/09_2024/8sn7_40615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/09_2024/8sn7_40615.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn7_40615/09_2024/8sn7_40615.cif" } 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8269 2.51 5 N 2713 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 33.174 72.290 48.380 1.00 72.35 S ATOM 12446 SG CYS K 51 31.114 69.178 47.704 1.00 73.71 S ATOM 12470 SG CYS K 54 32.901 70.989 44.890 1.00 79.16 S ATOM 12187 SG CYS K 16 22.600 66.502 53.978 1.00 79.23 S ATOM 12205 SG CYS K 19 20.009 64.339 55.691 1.00 76.33 S ATOM 12335 SG CYS K 36 23.168 65.453 57.650 1.00 74.99 S ATOM 12357 SG CYS K 39 23.514 62.918 55.146 1.00 76.41 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 9.27, per 1000 atoms: 0.63 Number of scatterers: 14600 At special positions: 0 Unit cell: (110.224, 131.472, 127.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3289 8.00 N 2713 7.00 C 8269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 4.06 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 62.9% alpha, 4.5% beta 136 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.543A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.683A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.919A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.864A pdb=" N ALA C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 150 Processing helix chain 'C' and resid 159 through 186 removed outlier: 3.548A pdb=" N LEU C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.795A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.602A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.697A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.006A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.833A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.635A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid -97 through -92 Processing helix chain 'G' and resid -86 through -76 Processing helix chain 'G' and resid -67 through -40 Processing helix chain 'G' and resid -34 through -23 removed outlier: 3.658A pdb=" N ASP G -23 " --> pdb=" O ALA G -27 " (cutoff:3.500A) Processing helix chain 'G' and resid -22 through -16 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.549A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.650A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.730A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.895A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.861A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 90 removed outlier: 3.567A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.676A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.132A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.575A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 143 removed outlier: 3.968A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.099A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 156 removed outlier: 8.078A pdb=" N ARG C 155 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 191 Processing sheet with id=AA6, first strand: chain 'C' and resid 214 through 215 removed outlier: 7.013A pdb=" N THR C 214 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.205A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid -71 through -70 removed outlier: 7.725A pdb=" N ARG G -71 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.558A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB3, first strand: chain 'M' and resid 5 through 6 491 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3222 1.33 - 1.45: 4431 1.45 - 1.57: 7184 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" CG LEU M 50 " pdb=" CD1 LEU M 50 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.08e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CB GLU C 174 " pdb=" CG GLU C 174 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 21582 1.56 - 3.12: 539 3.12 - 4.68: 28 4.68 - 6.24: 15 6.24 - 7.80: 7 Bond angle restraints: 22171 Sorted by residual: angle pdb=" C CYS K 31 " pdb=" N ASN K 32 " pdb=" CA ASN K 32 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C3' DG J -70 " pdb=" C2' DG J -70 " pdb=" C1' DG J -70 " ideal model delta sigma weight residual 101.60 105.65 -4.05 1.50e+00 4.44e-01 7.31e+00 angle pdb=" CB MET L 38 " pdb=" CG MET L 38 " pdb=" SD MET L 38 " ideal model delta sigma weight residual 112.70 120.02 -7.32 3.00e+00 1.11e-01 5.95e+00 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 125.89 -3.43 1.41e+00 5.03e-01 5.93e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 105.40 7.30 3.00e+00 1.11e-01 5.92e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 7270 35.74 - 71.48: 1318 71.48 - 107.22: 15 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 8605 sinusoidal: 5467 harmonic: 3138 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 41.30 178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 70.18 149.82 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CB GLU D 105 " pdb=" CG GLU D 105 " pdb=" CD GLU D 105 " pdb=" OE1 GLU D 105 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1777 0.032 - 0.065: 559 0.065 - 0.097: 128 0.097 - 0.129: 46 0.129 - 0.162: 6 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ASN K 32 " pdb=" N ASN K 32 " pdb=" C ASN K 32 " pdb=" CB ASN K 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 2513 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO L 61 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO K 38 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.027 2.00e-02 2.50e+03 1.15e-02 3.66e+00 pdb=" N9 DA I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1940 2.76 - 3.47: 19329 3.47 - 4.19: 38549 4.19 - 4.90: 60082 Nonbonded interactions: 119902 Sorted by model distance: nonbonded pdb=" N SER G-102 " pdb=" C SER H 123 " model vdw 1.330 3.350 nonbonded pdb=" N SER C 124 " pdb=" C SER D 123 " model vdw 1.330 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.210 2.496 nonbonded pdb=" N SER C 124 " pdb=" O SER D 123 " model vdw 2.250 3.120 nonbonded pdb=" N SER G-102 " pdb=" O SER H 123 " model vdw 2.252 3.120 ... (remaining 119897 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 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid -102 through 5) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.00 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: 1.540 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.170 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.004 0.048 15472 Z= 0.212 Angle : 0.567 7.799 22171 Z= 0.329 Chirality : 0.035 0.162 2516 Planarity : 0.004 0.073 1794 Dihedral : 25.759 178.704 6577 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.83 (0.26), residues: 1057 helix: 2.34 (0.21), residues: 627 sheet: -1.13 (0.72), residues: 41 loop : -0.41 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 77 HIS 0.004 0.001 HIS D 82 PHE 0.008 0.001 PHE E 78 TYR 0.025 0.002 TYR M 59 ARG 0.005 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8564 (ttmm) REVERT: E 76 GLN cc_start: 0.8261 (pp30) cc_final: 0.8002 (pp30) REVERT: H 34 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8899 (mtmm) REVERT: H 86 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7804 (mmt-90) REVERT: H 120 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8569 (ttpp) REVERT: L 63 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8253 (mttt) REVERT: L 114 ASN cc_start: 0.7881 (t0) cc_final: 0.7667 (m-40) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2695 time to fit residues: 82.9744 Evaluate side-chains 189 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G -29 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15472 Z= 0.257 Angle : 0.598 9.889 22171 Z= 0.342 Chirality : 0.037 0.165 2516 Planarity : 0.005 0.050 1794 Dihedral : 28.894 179.753 4413 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.08 % Allowed : 10.28 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.76 (0.27), residues: 1057 helix: 2.31 (0.21), residues: 649 sheet: -1.10 (0.80), residues: 34 loop : -0.68 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.011 0.001 PHE L 56 TYR 0.022 0.002 TYR D 83 ARG 0.006 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8268 (pp30) cc_final: 0.7959 (pp30) REVERT: E 120 MET cc_start: 0.8256 (mtp) cc_final: 0.8030 (mtt) REVERT: H 34 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8864 (mtmm) REVERT: H 86 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7816 (mmt-90) REVERT: H 120 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8612 (ttpt) REVERT: L 63 LYS cc_start: 0.8752 (mmtp) cc_final: 0.8532 (mttt) REVERT: L 127 TYR cc_start: 0.7672 (t80) cc_final: 0.7371 (t80) REVERT: L 135 ASN cc_start: 0.8464 (m-40) cc_final: 0.8220 (m-40) outliers start: 10 outliers final: 8 residues processed: 199 average time/residue: 0.3063 time to fit residues: 84.6482 Evaluate side-chains 191 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 13 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 92 GLN ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15472 Z= 0.314 Angle : 0.608 9.737 22171 Z= 0.348 Chirality : 0.037 0.147 2516 Planarity : 0.005 0.049 1794 Dihedral : 29.117 179.549 4413 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.16 % Allowed : 12.34 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.65 (0.26), residues: 1057 helix: 2.24 (0.21), residues: 645 sheet: -1.63 (0.72), residues: 33 loop : -0.67 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.010 0.002 PHE E 104 TYR 0.024 0.002 TYR K 84 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8582 (mm-30) REVERT: H 34 LYS cc_start: 0.9117 (mtmm) cc_final: 0.8879 (mtmm) REVERT: H 86 ARG cc_start: 0.8161 (mmt90) cc_final: 0.7842 (mmt-90) REVERT: H 120 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8610 (ttpt) REVERT: L 0 HIS cc_start: 0.7616 (t-90) cc_final: 0.7265 (t-90) REVERT: L 135 ASN cc_start: 0.8405 (m-40) cc_final: 0.8112 (m-40) REVERT: L 147 MET cc_start: 0.7123 (mpp) cc_final: 0.6600 (mpp) outliers start: 20 outliers final: 14 residues processed: 194 average time/residue: 0.3064 time to fit residues: 82.2358 Evaluate side-chains 198 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 92 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15472 Z= 0.241 Angle : 0.585 10.094 22171 Z= 0.335 Chirality : 0.036 0.160 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.137 179.683 4413 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.73 % Allowed : 14.29 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.79 (0.26), residues: 1057 helix: 2.34 (0.21), residues: 647 sheet: -1.56 (0.69), residues: 33 loop : -0.62 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.015 0.002 PHE L 62 TYR 0.021 0.002 TYR D 83 ARG 0.007 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8539 (mm-30) REVERT: H 34 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8866 (mtmm) REVERT: H 86 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7814 (mmt-90) REVERT: H 120 LYS cc_start: 0.9131 (ttpt) cc_final: 0.8651 (ttpt) REVERT: L 1 MET cc_start: 0.7518 (mmm) cc_final: 0.7217 (mmm) REVERT: L 73 ILE cc_start: 0.7786 (mp) cc_final: 0.7454 (tp) REVERT: L 92 GLN cc_start: 0.7131 (mm110) cc_final: 0.6492 (mm-40) REVERT: L 127 TYR cc_start: 0.7679 (t80) cc_final: 0.7420 (t80) REVERT: L 135 ASN cc_start: 0.8375 (m-40) cc_final: 0.8145 (m-40) REVERT: L 147 MET cc_start: 0.6960 (mpp) cc_final: 0.6396 (mpp) outliers start: 16 outliers final: 14 residues processed: 195 average time/residue: 0.3230 time to fit residues: 87.0449 Evaluate side-chains 200 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15472 Z= 0.224 Angle : 0.580 10.615 22171 Z= 0.332 Chirality : 0.035 0.159 2516 Planarity : 0.004 0.052 1794 Dihedral : 29.169 179.348 4413 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 15.37 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.27), residues: 1057 helix: 2.38 (0.21), residues: 648 sheet: -1.56 (0.74), residues: 33 loop : -0.56 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.014 0.001 PHE L 51 TYR 0.016 0.002 TYR H 83 ARG 0.005 0.000 ARG L 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8668 (pm20) cc_final: 0.8398 (pm20) REVERT: E 94 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8514 (mm-30) REVERT: H 34 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8886 (mtmm) REVERT: H 86 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7801 (mmt-90) REVERT: H 120 LYS cc_start: 0.9123 (ttpt) cc_final: 0.8636 (ttpt) REVERT: L 73 ILE cc_start: 0.7678 (mp) cc_final: 0.7305 (tp) REVERT: L 135 ASN cc_start: 0.8210 (m-40) cc_final: 0.7900 (m-40) REVERT: L 147 MET cc_start: 0.7096 (mpp) cc_final: 0.6611 (mpp) outliers start: 19 outliers final: 14 residues processed: 202 average time/residue: 0.3121 time to fit residues: 87.2898 Evaluate side-chains 200 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -29 GLN L 32 HIS L 46 GLN L 92 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15472 Z= 0.218 Angle : 0.593 10.731 22171 Z= 0.336 Chirality : 0.036 0.287 2516 Planarity : 0.004 0.048 1794 Dihedral : 29.185 179.078 4413 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.38 % Allowed : 16.13 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.91 (0.27), residues: 1057 helix: 2.44 (0.21), residues: 646 sheet: -1.93 (0.69), residues: 33 loop : -0.53 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.022 0.001 PHE L 62 TYR 0.018 0.002 TYR L 134 ARG 0.015 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8638 (pm20) cc_final: 0.8335 (pm20) REVERT: E 94 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8512 (mm-30) REVERT: H 34 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8874 (mtmm) REVERT: H 86 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7801 (mmt-90) REVERT: H 120 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8635 (ttpt) REVERT: L 73 ILE cc_start: 0.7664 (mp) cc_final: 0.7299 (tp) REVERT: L 135 ASN cc_start: 0.8276 (m-40) cc_final: 0.7980 (m-40) REVERT: L 147 MET cc_start: 0.6868 (mpp) cc_final: 0.6505 (mpp) outliers start: 22 outliers final: 17 residues processed: 201 average time/residue: 0.3133 time to fit residues: 87.4162 Evaluate side-chains 200 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.0000 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN L 32 HIS L 41 ASN L 46 GLN L 92 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15472 Z= 0.179 Angle : 0.573 10.456 22171 Z= 0.326 Chirality : 0.034 0.160 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.142 179.272 4413 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.84 % Allowed : 17.32 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.27), residues: 1057 helix: 2.51 (0.21), residues: 646 sheet: -1.93 (0.70), residues: 33 loop : -0.52 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 33 HIS 0.003 0.001 HIS E 39 PHE 0.013 0.001 PHE L 51 TYR 0.026 0.002 TYR L 45 ARG 0.011 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8290 (pm20) REVERT: E 94 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8454 (mm-30) REVERT: H 34 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8857 (mtmm) REVERT: H 86 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7768 (mmt-90) REVERT: H 120 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8624 (ttpt) REVERT: L 73 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7249 (tp) REVERT: L 135 ASN cc_start: 0.8414 (m-40) cc_final: 0.8212 (m-40) REVERT: L 147 MET cc_start: 0.7095 (mpp) cc_final: 0.6763 (mpp) outliers start: 17 outliers final: 13 residues processed: 193 average time/residue: 0.3100 time to fit residues: 83.3749 Evaluate side-chains 197 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS L 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15472 Z= 0.294 Angle : 0.610 11.502 22171 Z= 0.345 Chirality : 0.037 0.188 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.299 178.743 4413 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.27 % Allowed : 17.32 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.78 (0.27), residues: 1057 helix: 2.34 (0.21), residues: 649 sheet: -2.05 (0.71), residues: 33 loop : -0.61 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.010 0.002 PHE E 78 TYR 0.015 0.002 TYR L 134 ARG 0.008 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8675 (pm20) cc_final: 0.8335 (pm20) REVERT: B 25 ASN cc_start: 0.9011 (m-40) cc_final: 0.8804 (m-40) REVERT: E 94 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8576 (mm-30) REVERT: H 34 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8899 (mtmm) REVERT: H 86 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7807 (mmt-90) REVERT: H 120 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8607 (ttpp) REVERT: L 147 MET cc_start: 0.7068 (mpp) cc_final: 0.6769 (mpp) outliers start: 21 outliers final: 17 residues processed: 192 average time/residue: 0.3070 time to fit residues: 82.1297 Evaluate side-chains 201 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15472 Z= 0.256 Angle : 0.608 11.449 22171 Z= 0.343 Chirality : 0.036 0.174 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.309 178.884 4413 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 18.18 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.76 (0.27), residues: 1057 helix: 2.31 (0.21), residues: 655 sheet: -2.21 (0.65), residues: 39 loop : -0.58 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 33 HIS 0.004 0.001 HIS E 39 PHE 0.014 0.001 PHE L 51 TYR 0.019 0.002 TYR L 134 ARG 0.008 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8660 (pm20) cc_final: 0.8302 (pm20) REVERT: E 94 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8562 (mm-30) REVERT: H 34 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8910 (mtmm) REVERT: H 86 ARG cc_start: 0.8097 (mmt90) cc_final: 0.7798 (mmt-90) REVERT: H 120 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8599 (ttpp) REVERT: L 147 MET cc_start: 0.7050 (mpp) cc_final: 0.6775 (mpp) outliers start: 18 outliers final: 17 residues processed: 192 average time/residue: 0.3049 time to fit residues: 81.7497 Evaluate side-chains 197 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 GLN L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15472 Z= 0.231 Angle : 0.602 12.236 22171 Z= 0.341 Chirality : 0.035 0.177 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.294 178.951 4413 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.84 % Allowed : 18.72 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.82 (0.27), residues: 1057 helix: 2.34 (0.21), residues: 655 sheet: -2.33 (0.62), residues: 38 loop : -0.51 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 141 HIS 0.004 0.001 HIS E 39 PHE 0.034 0.002 PHE L 50 TYR 0.019 0.002 TYR L 134 ARG 0.008 0.000 ARG L 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8693 (pm20) cc_final: 0.8343 (pm20) REVERT: E 61 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8995 (mm) REVERT: E 94 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8548 (mm-30) REVERT: H 34 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8895 (mtmm) REVERT: H 86 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7788 (mmt-90) REVERT: H 120 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8625 (ttpt) REVERT: L 147 MET cc_start: 0.6921 (mpp) cc_final: 0.6700 (mpp) outliers start: 17 outliers final: 16 residues processed: 189 average time/residue: 0.3042 time to fit residues: 80.5031 Evaluate side-chains 196 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 0.0030 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.082018 restraints weight = 38177.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.083925 restraints weight = 22617.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.084100 restraints weight = 15605.914| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15472 Z= 0.189 Angle : 0.601 12.738 22171 Z= 0.338 Chirality : 0.035 0.237 2516 Planarity : 0.004 0.047 1794 Dihedral : 29.209 179.187 4413 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.73 % Allowed : 19.48 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.27), residues: 1057 helix: 2.45 (0.21), residues: 647 sheet: -1.75 (0.62), residues: 48 loop : -0.54 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 141 HIS 0.004 0.001 HIS E 39 PHE 0.017 0.001 PHE L 50 TYR 0.018 0.001 TYR K 64 ARG 0.010 0.000 ARG L 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.38 seconds wall clock time: 48 minutes 42.79 seconds (2922.79 seconds total)