Starting phenix.real_space_refine on Thu Feb 15 10:46:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/02_2024/6se6_10152.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/02_2024/6se6_10152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/02_2024/6se6_10152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/02_2024/6se6_10152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/02_2024/6se6_10152.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/02_2024/6se6_10152.pdb" } resolution = 3.5 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6706 2.51 5 N 2263 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "V ARG 522": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12068 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" 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: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "V" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 6.60, per 1000 atoms: 0.55 Number of scatterers: 12068 At special positions: 0 Unit cell: (78, 120.25, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2801 8.00 N 2263 7.00 C 6706 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 69.4% alpha, 2.3% beta 144 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 4.271A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.526A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.808A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.547A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.705A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.234A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.668A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.673A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.458A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.599A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.836A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.871A 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 104 through 122 removed outlier: 3.594A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 4.192A pdb=" N LYS E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.565A pdb=" N VAL E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.785A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 4.276A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.745A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.631A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 4.070A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.654A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.990A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.771A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.511A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.594A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.073A pdb=" N ASN A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.658A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.678A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 351 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1874 1.32 - 1.44: 4461 1.44 - 1.56: 5947 1.56 - 1.68: 580 1.68 - 1.79: 18 Bond restraints: 12880 Sorted by residual: bond pdb=" CB VAL C 27 " pdb=" CG2 VAL C 27 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.27e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" CB THR F 73 " pdb=" CG2 THR F 73 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL G 27 " pdb=" CG2 VAL G 27 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.74e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.79: 1211 104.79 - 112.10: 6990 112.10 - 119.41: 4302 119.41 - 126.72: 5310 126.72 - 134.03: 824 Bond angle restraints: 18637 Sorted by residual: angle pdb=" C THR A 79 " pdb=" N ARG A 80 " pdb=" CA ARG A 80 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C ARG A 44 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta sigma weight residual 122.46 127.70 -5.24 1.41e+00 5.03e-01 1.38e+01 angle pdb=" CA TRP V 530 " pdb=" CB TRP V 530 " pdb=" CG TRP V 530 " ideal model delta sigma weight residual 113.60 120.65 -7.05 1.90e+00 2.77e-01 1.38e+01 angle pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sigma weight residual 120.20 125.57 -5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " pdb=" P DT I -28 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 ... (remaining 18632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 5551 35.73 - 71.45: 1381 71.45 - 107.18: 18 107.18 - 142.90: 6 142.90 - 178.63: 2 Dihedral angle restraints: 6958 sinusoidal: 4740 harmonic: 2218 Sorted by residual: 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 -140.00 38.63 -178.63 1 3.50e+01 8.16e-04 1.57e+01 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 75.72 144.28 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 94.35 125.65 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 6955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1290 0.047 - 0.093: 600 0.093 - 0.140: 167 0.140 - 0.187: 51 0.187 - 0.233: 6 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CG LEU G 97 " pdb=" CB LEU G 97 " pdb=" CD1 LEU G 97 " pdb=" CD2 LEU G 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2111 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.054 2.00e-02 2.50e+03 2.34e-02 1.64e+01 pdb=" N9 DG I 26 " 0.056 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.043 2.00e-02 2.50e+03 1.98e-02 1.18e+01 pdb=" N9 DG I 28 " 0.049 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.016 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -26 " 0.044 2.00e-02 2.50e+03 2.06e-02 1.07e+01 pdb=" N1 DT I -26 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DT I -26 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT I -26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I -26 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT I -26 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I -26 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I -26 " -0.008 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2460 2.78 - 3.31: 10073 3.31 - 3.84: 24303 3.84 - 4.37: 27108 4.37 - 4.90: 38480 Nonbonded interactions: 102424 Sorted by model distance: nonbonded pdb=" O2 DC I -4 " pdb=" N2 DG J 4 " model vdw 2.247 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.249 2.496 nonbonded pdb=" O2 DC I -56 " pdb=" N2 DG J 56 " model vdw 2.264 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.268 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.275 2.496 ... (remaining 102419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 116) } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 8.340 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 40.210 Find NCS groups from input model: 0.430 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.010 0.095 12880 Z= 0.593 Angle : 0.998 12.172 18637 Z= 0.571 Chirality : 0.059 0.233 2114 Planarity : 0.008 0.074 1347 Dihedral : 27.962 178.630 5528 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.22), residues: 753 helix: -2.55 (0.16), residues: 508 sheet: None (None), residues: 0 loop : -2.06 (0.30), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 530 HIS 0.015 0.002 HIS F 75 PHE 0.016 0.003 PHE A 84 TYR 0.022 0.003 TYR G 50 ARG 0.008 0.001 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7960 (pp30) cc_final: 0.7738 (pm20) REVERT: A 96 GLU cc_start: 0.8131 (tp30) cc_final: 0.7898 (mm-30) REVERT: B 53 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 88 TYR cc_start: 0.8395 (m-10) cc_final: 0.8023 (m-10) REVERT: C 56 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8308 (tm-30) REVERT: C 75 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8644 (mmtm) REVERT: D 59 MET cc_start: 0.8838 (tpp) cc_final: 0.8635 (tpp) REVERT: D 63 ASN cc_start: 0.8898 (t0) cc_final: 0.8215 (t0) REVERT: D 67 ASN cc_start: 0.8841 (m-40) cc_final: 0.8383 (t0) REVERT: D 68 ASP cc_start: 0.8095 (t70) cc_final: 0.7869 (t0) REVERT: D 71 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 76 GLU cc_start: 0.8063 (tp30) cc_final: 0.7842 (tp30) REVERT: E 73 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 64 ASN cc_start: 0.8302 (t0) cc_final: 0.7761 (t0) REVERT: F 88 TYR cc_start: 0.8906 (m-10) cc_final: 0.7888 (m-10) REVERT: F 91 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8898 (ttpp) REVERT: F 93 GLN cc_start: 0.7584 (mt0) cc_final: 0.6771 (mt0) REVERT: G 64 GLU cc_start: 0.8568 (tp30) cc_final: 0.8344 (tp30) REVERT: H 42 TYR cc_start: 0.7781 (t80) cc_final: 0.7298 (t80) REVERT: H 68 ASP cc_start: 0.8689 (t0) cc_final: 0.8459 (t0) REVERT: H 83 TYR cc_start: 0.8742 (m-10) cc_final: 0.8298 (m-80) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3734 time to fit residues: 113.9190 Evaluate side-chains 180 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 27 GLN B 93 GLN C 31 HIS C 73 ASN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12880 Z= 0.193 Angle : 0.603 5.839 18637 Z= 0.359 Chirality : 0.034 0.174 2114 Planarity : 0.004 0.045 1347 Dihedral : 30.745 175.601 4019 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.88 % Allowed : 18.03 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 753 helix: 0.08 (0.21), residues: 514 sheet: None (None), residues: 0 loop : -1.68 (0.32), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 530 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.015 0.002 TYR D 40 ARG 0.008 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 220 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7966 (pp30) cc_final: 0.7753 (pm20) REVERT: A 127 GLN cc_start: 0.8041 (tp40) cc_final: 0.7840 (tp40) REVERT: B 53 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 88 TYR cc_start: 0.8347 (m-10) cc_final: 0.8016 (m-10) REVERT: B 91 LYS cc_start: 0.8797 (tttt) cc_final: 0.8436 (tptp) REVERT: C 56 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8284 (tm-30) REVERT: C 57 TYR cc_start: 0.9049 (t80) cc_final: 0.8792 (t80) REVERT: C 61 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 71 ARG cc_start: 0.8573 (ttm110) cc_final: 0.8367 (ttp80) REVERT: D 34 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8454 (mptt) REVERT: D 35 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6728 (mm-30) REVERT: D 63 ASN cc_start: 0.8532 (t0) cc_final: 0.7938 (t0) REVERT: D 67 ASN cc_start: 0.8669 (m-40) cc_final: 0.8336 (t0) REVERT: D 71 GLU cc_start: 0.8203 (tm-30) cc_final: 0.8001 (tm-30) REVERT: E 132 ILE cc_start: 0.9016 (tt) cc_final: 0.8767 (tt) REVERT: F 50 ILE cc_start: 0.8328 (mt) cc_final: 0.8038 (tt) REVERT: F 64 ASN cc_start: 0.8240 (t0) cc_final: 0.7569 (t0) REVERT: F 91 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8857 (ttpp) REVERT: F 93 GLN cc_start: 0.7640 (mt0) cc_final: 0.6509 (mt0) REVERT: G 64 GLU cc_start: 0.8508 (tp30) cc_final: 0.8054 (tp30) REVERT: G 72 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8131 (p0) REVERT: G 92 GLU cc_start: 0.7111 (tt0) cc_final: 0.6722 (tt0) REVERT: H 42 TYR cc_start: 0.7866 (t80) cc_final: 0.7428 (t80) REVERT: H 68 ASP cc_start: 0.8561 (t0) cc_final: 0.8327 (t0) REVERT: H 83 TYR cc_start: 0.8535 (m-10) cc_final: 0.8173 (m-80) outliers start: 12 outliers final: 8 residues processed: 222 average time/residue: 0.2824 time to fit residues: 84.9890 Evaluate side-chains 199 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 35 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12880 Z= 0.342 Angle : 0.645 8.605 18637 Z= 0.376 Chirality : 0.037 0.159 2114 Planarity : 0.004 0.037 1347 Dihedral : 30.661 173.622 4019 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.23 % Allowed : 20.85 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.29), residues: 753 helix: 1.04 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.83 (0.32), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 530 HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE E 101 TYR 0.025 0.002 TYR D 83 ARG 0.006 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8007 (pp30) cc_final: 0.7747 (pm20) REVERT: A 127 GLN cc_start: 0.8195 (tp40) cc_final: 0.7982 (tp40) REVERT: B 53 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8276 (tm-30) REVERT: B 91 LYS cc_start: 0.8820 (tttt) cc_final: 0.8518 (tptp) REVERT: C 56 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8540 (tm-30) REVERT: C 63 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9473 (mm) REVERT: D 34 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8532 (mptt) REVERT: D 63 ASN cc_start: 0.8722 (t0) cc_final: 0.8196 (t0) REVERT: D 67 ASN cc_start: 0.8776 (m-40) cc_final: 0.8412 (t0) REVERT: F 64 ASN cc_start: 0.8354 (t0) cc_final: 0.7715 (t0) REVERT: F 91 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8886 (ttpp) REVERT: F 93 GLN cc_start: 0.7795 (mt0) cc_final: 0.6687 (mt0) REVERT: G 92 GLU cc_start: 0.7219 (tt0) cc_final: 0.6996 (tt0) REVERT: H 42 TYR cc_start: 0.7925 (t80) cc_final: 0.7660 (t80) REVERT: H 68 ASP cc_start: 0.8667 (t0) cc_final: 0.8442 (t0) REVERT: H 83 TYR cc_start: 0.8595 (m-10) cc_final: 0.8326 (m-80) outliers start: 27 outliers final: 22 residues processed: 193 average time/residue: 0.2723 time to fit residues: 71.9421 Evaluate side-chains 200 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12880 Z= 0.187 Angle : 0.564 5.510 18637 Z= 0.338 Chirality : 0.033 0.156 2114 Planarity : 0.003 0.036 1347 Dihedral : 30.530 173.618 4019 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.98 % Allowed : 24.61 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 753 helix: 1.60 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 530 HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE A 78 TYR 0.018 0.002 TYR D 83 ARG 0.004 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8084 (tp40) cc_final: 0.7811 (tp40) REVERT: B 91 LYS cc_start: 0.8753 (tttt) cc_final: 0.8473 (tptp) REVERT: C 56 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 57 TYR cc_start: 0.8980 (t80) cc_final: 0.8738 (t80) REVERT: C 63 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9410 (mm) REVERT: D 34 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8600 (mptt) REVERT: D 63 ASN cc_start: 0.8413 (t0) cc_final: 0.7937 (t0) REVERT: D 67 ASN cc_start: 0.8634 (m-40) cc_final: 0.8321 (t0) REVERT: D 71 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7789 (tt0) REVERT: D 76 GLU cc_start: 0.7729 (tp30) cc_final: 0.7526 (tp30) REVERT: E 45 GLN cc_start: 0.8390 (pt0) cc_final: 0.8026 (pp30) REVERT: F 50 ILE cc_start: 0.8356 (mt) cc_final: 0.8074 (tt) REVERT: F 64 ASN cc_start: 0.8344 (t0) cc_final: 0.8020 (t0) REVERT: F 91 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8887 (ttpp) REVERT: G 24 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8074 (mp10) REVERT: G 92 GLU cc_start: 0.6798 (tt0) cc_final: 0.6147 (tt0) outliers start: 19 outliers final: 10 residues processed: 212 average time/residue: 0.2632 time to fit residues: 77.2037 Evaluate side-chains 197 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12880 Z= 0.396 Angle : 0.661 6.150 18637 Z= 0.382 Chirality : 0.038 0.151 2114 Planarity : 0.004 0.034 1347 Dihedral : 30.733 169.438 4019 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 6.11 % Allowed : 25.08 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.30), residues: 753 helix: 1.48 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.52 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 530 HIS 0.008 0.001 HIS F 75 PHE 0.010 0.002 PHE E 84 TYR 0.054 0.003 TYR B 88 ARG 0.007 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8288 (tp40) cc_final: 0.8015 (tp-100) REVERT: B 91 LYS cc_start: 0.8828 (tttt) cc_final: 0.8508 (tptp) REVERT: C 56 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8555 (tm-30) REVERT: C 63 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9460 (mm) REVERT: D 34 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8555 (mptt) REVERT: D 63 ASN cc_start: 0.8798 (t0) cc_final: 0.8304 (t0) REVERT: D 67 ASN cc_start: 0.8801 (m-40) cc_final: 0.8424 (t0) REVERT: D 76 GLU cc_start: 0.8021 (tp30) cc_final: 0.7809 (tp30) REVERT: E 53 LYS cc_start: 0.9304 (tppp) cc_final: 0.9090 (tppt) REVERT: F 27 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8201 (tm-30) REVERT: F 64 ASN cc_start: 0.8434 (t0) cc_final: 0.7657 (t0) REVERT: F 91 LYS cc_start: 0.9235 (ttmt) cc_final: 0.9006 (ttpp) REVERT: F 93 GLN cc_start: 0.7889 (mt0) cc_final: 0.6583 (mt0) REVERT: G 92 GLU cc_start: 0.7308 (tt0) cc_final: 0.6659 (tt0) REVERT: G 111 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7094 (pt) REVERT: H 106 LEU cc_start: 0.9381 (mt) cc_final: 0.8994 (mt) outliers start: 39 outliers final: 31 residues processed: 195 average time/residue: 0.2601 time to fit residues: 70.3216 Evaluate side-chains 204 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12880 Z= 0.274 Angle : 0.606 7.337 18637 Z= 0.357 Chirality : 0.035 0.149 2114 Planarity : 0.004 0.032 1347 Dihedral : 30.649 168.573 4019 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.70 % Allowed : 28.06 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 753 helix: 1.66 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 47 HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE A 78 TYR 0.050 0.003 TYR B 88 ARG 0.005 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8241 (tp40) cc_final: 0.7947 (tp-100) REVERT: B 91 LYS cc_start: 0.8749 (tttt) cc_final: 0.8438 (tptp) REVERT: B 93 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: C 56 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8505 (tm-30) REVERT: C 63 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9445 (mm) REVERT: D 34 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8551 (mptt) REVERT: D 63 ASN cc_start: 0.8657 (t0) cc_final: 0.8189 (t0) REVERT: D 67 ASN cc_start: 0.8755 (m-40) cc_final: 0.8406 (t0) REVERT: D 71 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7822 (tt0) REVERT: E 53 LYS cc_start: 0.9299 (tppp) cc_final: 0.9087 (tppt) REVERT: F 64 ASN cc_start: 0.8444 (t0) cc_final: 0.8070 (t0) REVERT: F 91 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8916 (ttpp) REVERT: G 92 GLU cc_start: 0.7294 (tt0) cc_final: 0.6658 (tt0) REVERT: G 111 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6972 (pt) REVERT: H 106 LEU cc_start: 0.9337 (mt) cc_final: 0.8992 (mt) outliers start: 30 outliers final: 24 residues processed: 195 average time/residue: 0.2560 time to fit residues: 69.2220 Evaluate side-chains 204 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.8273 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12880 Z= 0.199 Angle : 0.581 9.115 18637 Z= 0.341 Chirality : 0.033 0.149 2114 Planarity : 0.003 0.033 1347 Dihedral : 30.497 165.380 4019 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.66 % Allowed : 30.72 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.30), residues: 753 helix: 1.87 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE A 78 TYR 0.044 0.002 TYR D 83 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8139 (tp40) cc_final: 0.7862 (tp40) REVERT: B 91 LYS cc_start: 0.8756 (tttt) cc_final: 0.8482 (tptp) REVERT: C 56 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 57 TYR cc_start: 0.8992 (t80) cc_final: 0.8764 (t80) REVERT: C 63 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9335 (mm) REVERT: D 34 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8555 (mptt) REVERT: D 63 ASN cc_start: 0.8437 (t0) cc_final: 0.8005 (t0) REVERT: D 67 ASN cc_start: 0.8695 (m-40) cc_final: 0.8406 (t0) REVERT: D 71 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7849 (tt0) REVERT: E 53 LYS cc_start: 0.9269 (tppp) cc_final: 0.9064 (tppt) REVERT: F 50 ILE cc_start: 0.8414 (mt) cc_final: 0.8030 (tt) REVERT: F 64 ASN cc_start: 0.8460 (t0) cc_final: 0.8126 (t0) REVERT: F 91 LYS cc_start: 0.9150 (ttmt) cc_final: 0.8886 (ttpp) REVERT: G 24 GLN cc_start: 0.8535 (mm-40) cc_final: 0.7980 (mp10) REVERT: G 92 GLU cc_start: 0.7033 (tt0) cc_final: 0.6338 (tt0) REVERT: G 111 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7052 (pt) REVERT: H 106 LEU cc_start: 0.9267 (mt) cc_final: 0.8914 (mt) outliers start: 17 outliers final: 14 residues processed: 194 average time/residue: 0.2641 time to fit residues: 72.1204 Evaluate side-chains 199 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12880 Z= 0.188 Angle : 0.570 8.182 18637 Z= 0.336 Chirality : 0.032 0.171 2114 Planarity : 0.003 0.037 1347 Dihedral : 30.392 159.399 4019 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.29 % Allowed : 30.72 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 753 helix: 2.05 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.20 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.007 0.001 HIS F 75 PHE 0.015 0.001 PHE A 78 TYR 0.043 0.002 TYR D 83 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.8251 (m-80) cc_final: 0.7971 (m-10) REVERT: A 127 GLN cc_start: 0.8102 (tp40) cc_final: 0.7805 (tp40) REVERT: B 79 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8362 (ttpp) REVERT: B 91 LYS cc_start: 0.8819 (tttt) cc_final: 0.8533 (tptp) REVERT: C 56 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8230 (tm-30) REVERT: C 57 TYR cc_start: 0.8937 (t80) cc_final: 0.8702 (t80) REVERT: D 34 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8543 (mptt) REVERT: D 63 ASN cc_start: 0.8422 (t0) cc_final: 0.7958 (t0) REVERT: D 67 ASN cc_start: 0.8656 (m-40) cc_final: 0.8447 (t0) REVERT: D 71 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7846 (tt0) REVERT: F 50 ILE cc_start: 0.8308 (mt) cc_final: 0.8084 (tt) REVERT: F 64 ASN cc_start: 0.8426 (t0) cc_final: 0.8083 (t0) REVERT: F 91 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8949 (ttpp) REVERT: G 24 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8141 (mp10) REVERT: G 92 GLU cc_start: 0.6971 (tt0) cc_final: 0.6320 (tt0) REVERT: G 111 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7076 (pt) REVERT: H 106 LEU cc_start: 0.9235 (mt) cc_final: 0.8878 (mt) outliers start: 21 outliers final: 17 residues processed: 194 average time/residue: 0.2458 time to fit residues: 66.8300 Evaluate side-chains 199 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12880 Z= 0.282 Angle : 0.622 7.217 18637 Z= 0.361 Chirality : 0.035 0.168 2114 Planarity : 0.004 0.032 1347 Dihedral : 30.494 160.745 4019 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.13 % Allowed : 31.35 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.30), residues: 753 helix: 1.90 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.24 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 47 HIS 0.007 0.001 HIS F 75 PHE 0.015 0.002 PHE A 84 TYR 0.057 0.003 TYR D 83 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.008 Fit side-chains REVERT: A 127 GLN cc_start: 0.8256 (tp40) cc_final: 0.7987 (tp40) REVERT: B 44 LYS cc_start: 0.8370 (tttt) cc_final: 0.7757 (tttt) REVERT: B 79 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8343 (ttpp) REVERT: B 91 LYS cc_start: 0.8839 (tttt) cc_final: 0.8370 (tptp) REVERT: C 56 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 63 ASN cc_start: 0.8649 (t0) cc_final: 0.8178 (t0) REVERT: F 64 ASN cc_start: 0.8406 (t0) cc_final: 0.7558 (t0) REVERT: F 91 LYS cc_start: 0.9174 (ttmt) cc_final: 0.8942 (ttpp) REVERT: F 93 GLN cc_start: 0.7962 (mt0) cc_final: 0.6769 (mt0) REVERT: G 24 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8014 (mp10) REVERT: G 92 GLU cc_start: 0.7343 (tt0) cc_final: 0.6967 (tt0) REVERT: G 111 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7122 (pt) outliers start: 20 outliers final: 19 residues processed: 182 average time/residue: 0.2591 time to fit residues: 65.5313 Evaluate side-chains 191 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12880 Z= 0.213 Angle : 0.603 7.891 18637 Z= 0.352 Chirality : 0.033 0.160 2114 Planarity : 0.004 0.036 1347 Dihedral : 30.405 164.188 4019 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.66 % Allowed : 32.45 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 753 helix: 1.93 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE A 84 TYR 0.076 0.003 TYR D 83 ARG 0.006 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.8372 (m-80) cc_final: 0.8089 (m-10) REVERT: A 127 GLN cc_start: 0.8156 (tp40) cc_final: 0.7870 (tp40) REVERT: B 79 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8365 (ttpp) REVERT: B 91 LYS cc_start: 0.8775 (tttt) cc_final: 0.8556 (tptp) REVERT: C 56 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8214 (tm-30) REVERT: C 57 TYR cc_start: 0.8976 (t80) cc_final: 0.8720 (t80) REVERT: D 34 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8475 (mptt) REVERT: D 63 ASN cc_start: 0.8498 (t0) cc_final: 0.8017 (t0) REVERT: D 67 ASN cc_start: 0.8691 (m-40) cc_final: 0.8456 (t0) REVERT: D 71 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7792 (tt0) REVERT: F 50 ILE cc_start: 0.8435 (mt) cc_final: 0.8067 (tt) REVERT: F 64 ASN cc_start: 0.8418 (t0) cc_final: 0.8057 (t0) REVERT: F 91 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8889 (ttpp) REVERT: G 24 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7976 (mp10) REVERT: G 92 GLU cc_start: 0.7093 (tt0) cc_final: 0.6747 (tt0) REVERT: G 111 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7076 (pt) outliers start: 17 outliers final: 15 residues processed: 189 average time/residue: 0.2709 time to fit residues: 70.3546 Evaluate side-chains 195 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.085484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059332 restraints weight = 40723.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061198 restraints weight = 20167.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062406 restraints weight = 13578.982| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12880 Z= 0.260 Angle : 0.621 8.390 18637 Z= 0.361 Chirality : 0.034 0.166 2114 Planarity : 0.003 0.034 1347 Dihedral : 30.470 167.126 4019 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.51 % Allowed : 32.76 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.30), residues: 753 helix: 1.92 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.10 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 47 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.001 PHE A 84 TYR 0.051 0.002 TYR D 83 ARG 0.006 0.000 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.63 seconds wall clock time: 40 minutes 40.99 seconds (2440.99 seconds total)